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--- bioinformatic_tools_to_detect_microsatellites_loci_from_genomic_data [2011/09/15 20:43]
tiagosobreira
+++ bioinformatic_tools_to_detect_microsatellites_loci_from_genomic_data [2013/08/08 19:21] (current)
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@@ Line 10: / Line 10: @@
 ^ Name ^ Year released ^ Latest update ^ Number of citations ^ Original publication ^ Repeats detected ^ Algorithm ^ Parameters ^ Input file ^ Output file ^ Detect imperfect or compound loci ^ Design primers ^ Online access ^ Interface (GUI or command-line) ^ Platform ^ language ^ Speed ^ Special Features ^ Limitations ^
-^Sputnik and Sputnik II     | 1994     | 2005     | [[http://scholar.google.ca/scholar?cites=2036014199810014882&as_sdt=2005&sciodt=0,5&hl=fr|124]]     | Abajian, 1994, with modifications in La Rota et al. 2005(([[http://www.biomedcentral.com/1471-2164/6/23|La Rota, M., Kantety, R., Yu, J.-K., and Sorrells, M. (2005). Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley. BMC Genomics 6, 23.]]))     | 2 to 5 bp only     | Recursive     | ?     | One file with one sequence     | Resulting hits are written to stdout along with their position in the sequence, length, and score     | Yes, Insertions, mismatches and deletions and compound     | ?     | ?     | ? [[http://espressosoftware.com/sputnik/index.html|Download]], SputnikII modified in 2005 [[http://wheat.pw.usda.gov/ITMI/EST-SSR/LaRota/|Download]]     | Windows     | C     | Execution time is dependent on the sequence composition     |      | Automated statistical analysis files not generated.     |     |
+^Sputnik and Sputnik II     | 1994     | 2005     | [[http://scholar.google.ca/scholar?cites=2036014199810014882&as_sdt=2005&sciodt=0,5&hl=fr|124]]     | Abajian, 1994, with modifications in La Rota et al. 2005(([[http://www.biomedcentral.com/1471-2164/6/23|La Rota, M., Kantety, R., Yu, J.-K., and Sorrells, M. (2005). Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley. BMC Genomics 6, 23.]]))     | 2 to 5 bp, or 1 to 5 bp in Morgante et al 2002(([[http://www.nature.com/doifinder/10.1038/ng822|Morgante, M., Hanafey, M., and Powell, W. (2002). Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nature Genetics 30, 194-200.]]))     | Recursive     | Match bonus and mismatch penalty, the validation score, the fail score, the maximum number of recursions, the minimum percentage of perfection, and the period size.     | One file with one sequence     | Resulting hits are written to stdout along with their position in the sequence, length, and score     | Yes, Insertions, mismatches and deletions and compound     | ?     | ?     | ? [[http://espressosoftware.com/sputnik/index.html|Download]], SputnikII modified in 2005 [[http://wheat.pw.usda.gov/ITMI/EST-SSR/LaRota/|Download]]     | Windows     | C     | Execution time is dependent on the sequence composition     |      | Automated statistical analysis files not generated.     |     |
 ^Not named     | 1998     | ?     | [[http://scholar.google.ca/scholar?cites=2876768191293615039&as_sdt=2005&sciodt=0,5&hl=fr|37]]     | Sagot and Myers 1998(([[http://www.liebertonline.com/doi/abs/10.1089/cmb.1998.5.539|Sagot, M.-F., and Myers, E. W. (1998). Identifying Satellites and Periodic Repetitions in Biological Sequences. Journal of Computational Biology 5, 539-553.]]))     | Detect repeats of fixed length, of 2 to 45 bp long per unit.     | Exhaustive     | Minimal size of a repeat (min_repeat),  minimum number of repeats within a TR (max-range), ? (max-jump)     | ?     | ?     | Yes, substitutions and indels     | No     | No     | ?     | ?     | ?     | Execution time increases with the number of TR detected     | Can be adapted to finding TR in protein sequences; and to identifying mixed direct-inverse TR.     | Does not detect duplicated genes     |     |
 ^TEIRESIAS     | 1998     | ?     | [[http://scholar.google.ca/scholar?cites=8485486606296648212&as_sdt=2005&sciodt=0,5&hl=fr|502]]     |Rigoustos et al 1998(([[http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/14.1.55|Rigoutsos, I., and Floratos, A. (1998). Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm. Bioinformatics 14, 55-67.]]))     | Detects nested TR     | Heuristic     | L (length of interrogated sequence) and W (length of one unit) and threshold K (length of the unit going to verification step)     | One file with multiple sequences.     | ?     | Yes, only substitutions (not indels)     | no     | No     | ? Available upon request to the [[mailto:[email protected];[email protected]|authors]] | ?     | ?     | Execution time increases quasi-linearly with length of units (W) and length of interrogated sequence (L)     | Motifs are guaranteed to be maximal in length and composition. Can identify duplicated genes. Can search in amino acid sequences.     | ?     |     |
-^TRF     | 1999     | 2004     | [[http://scholar.google.ca/scholar?cites=2912855801419178739&as_sdt=2005&sciodt=0,5&hl=fr|1487]]     | Benson 1999(([[http://www.nar.oupjournals.org/cgi/doi/10.1093/nar/27.2.573|Benson, G. (1999). Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Research 27, 573-580.]]))     | >6 bp repeats     | Heuristic; based on the alignment procedure and k-tuples.     | (i) alignment weights for match, mismatch and indels; (ii) pM and pI; (iii) a minimum size for patterns to report; (iv) a minimum alignment score to report.     | One file with one sequence     | A summary table file with location and statistical properties of the TR found. The other file is alignment of each repeat with its consensus sequence     | Yes, imperfect and compound     |      | [[http://tandem.bu.edu/trf/trf.submit.options.html|Yes]]     | ? [[http://tandem.bu.edu/trf/trf.download.html|Download]]     | platform independent     | Source code not available     | Slow. Execution time is exponential to the number of repeats detected     | Able to detect TR in a wide range of size and copy number     | Does not accept sequences longer than 5 Mb; Automated statistical analysis files not generated; output files are difficult to manage.     |     |
+^TRF     | 1999     | 2004     | [[http://scholar.google.ca/scholar?cites=2912855801419178739&as_sdt=2005&sciodt=0,5&hl=fr|1487]]     | Benson 1999(([[http://www.nar.oupjournals.org/cgi/doi/10.1093/nar/27.2.573|Benson, G. (1999). Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Research 27, 573-580.]]))     | >6 bp repeats     | Heuristic; based on the alignment procedure and k-tuples.     | a) alignment weights for match, mismatch and indels; b) pM and pI; c) minimum size for patterns to report; d) minimum alignment score (threshold).     | One file with one sequence     | A summary table file with location and statistical properties of the TR found. The other file is alignment of each repeat with its consensus sequence     | Yes, imperfect and compound     |      | [[http://tandem.bu.edu/trf/trf.submit.options.html|Yes]]     | ? [[http://tandem.bu.edu/trf/trf.download.html|Download]]     | platform independent     | Source code not available     | Slow. Execution time is exponential to the number of repeats detected     | Able to detect TR in a wide range of size and copy number     | Does not accept sequences longer than 5 Mb; Automated statistical analysis files not generated; output files are difficult to manage.     |     |
 ^Not named     | 2001     | ?     | [[http://scholar.google.ca/scholar?cites=1469843543430168168&as_sdt=2005&sciodt=0,5&hl=fr|94]]     | Landau et al 2001(([[http://www.liebertonline.com/doi/abs/10.1089/106652701300099038|Landau, G. M., Schmidt, J. P., and Sokol, D. (2001). An algorithm for approximate tandem repeats. Journal of Computational Biology 8, 1-18.]]))     | ?     | Exhaustive; uses Hamming distance (k mismatches) and edit distance (k differences)     | ?     | ?     | ?     | Yes, substitutions (but not indels)     |      | No     | ? Available upon request to the [[mailto:[email protected]|authors]]     | ?     | ?     | ?     | ?     | ?     |     |
 ^REPuter     | 2001     | 2005     | [[http://scholar.google.ca/scholar?cites=16580208599321300202&as_sdt=2005&sciodt=0,5&hl=fr|341]]     | Kurtz et al 2001(([[http://www.nar.oupjournals.org/cgi/doi/10.1093/nar/29.22.4633|Kurtz, S. (2001). REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Research 29, 4633-4642.]]))     | Detect repeats of fixed length. Repeats need not to be in tandem     | Heuristic; uses the Hamming distance model and the edit distance model     | sequencetype, smap, direct, palindromic, length, hamming, edit, best, content, identity, evalue (error threshold k ≥ 0 and a length threshold l > 0 are given)     | Limit of 5 Mb in the online version, DNA or protein     | Statistical and graphical analysis     | Yes, imperfect including substitutions and compound     |      | [[http://bibiserv.techfak.uni-bielefeld.de/reputer/submission.html    |Yes]]     | Command-line, [[http://bibiserv.techfak.uni-bielefeld.de/reputer/|Download]]     | Linux, OSX, Solaris, Irix and Alpha     | ?     | ?     | Nucleic acid or amino acid sequence; combine linear time efficiency with exhaustive analysis     | Is not primarily designed for microsatellites     |     |
@@ Line 19: / Line 19: @@
 ^ComplexTR     | 2002     | 2005     | [[http://scholar.google.ca/scholar?cites=10462322261601920203&as_sdt=2005&sciodt=0,5&hl=fr|33]]     | Hauth and Joseph 2002(([[http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/18.suppl_1.S31|Hauth, A. M., and Joseph, D. A. (2002). Beyond tandem repeats: complex pattern structures and distant regions of similarity. Bioinformatics 18, S31-S37.]]))     | Long repeats, variable length TR (VLTRs) and multiperiod TR (MPTRs)     | Seed-extension technique; analyses k-length substrings     | ?     | One file with one sequence     | HTML page with detailed characterization of each TR region     |      |      | The [[http://megasun.bch.umontreal.ca/People/ahauth/tools/    |web access]] is not functioning     | Command-line [[http://megasun.bch.umontreal.ca/People/ahauth/tools/|Download]]     | ?     | C++, perl.  Tandem repeat identification code (C++); Web Interface via CGI scripts (perl)     | ?     | Identifies duplicated genes and pseudogenes     | ?     |     |
 ^TROLL     | 2002     | ?     | [[http://scholar.google.ca/scholar?cites=12253928681016535900&as_sdt=2005&sciodt=0,5&hl=fr|125]]     | Castelo et al 2002(([[http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/18.4.634|Castelo, A. T., Martins, W., and Gao, G. R. (2002). TROLL--Tandem Repeat Occurrence Locator. Bioinformatics 18, 634-636.]])) and Martins et al. 2006(([[http://www.nar.oxfordjournals.org/cgi/doi/10.1093/nar/gnj030|Martins, W. (2006). New softwares for automated microsatellite marker development. Nucleic Acids Research 34, e31-e31.]]))     | Only searches for predefined motifs     | Dictionary approach and the failure links for mismatches     | Minimum length desired; maximum motif length; file containg the motif list;     | One file with one sequence     | Can be easily imported to other applications     | Yes, imperfect and compound (indels?)     | Yes, with Primer3     | No     | Command-line [[http://finder.sourceforge.net|Download]]     | Linux     | C++ (Tcp/Tk script)     | ?     | ?     | ?     |     |
-^ATRHunter      | 2004     | 2003     | [[http://scholar.google.ca/scholar?cites=11187065548778505423&as_sdt=2005&sciodt=0,5&hl=fr|47]]     | [[http://bioinfo.cs.technion.ac.il/atrhunter/ATR.pdf|Wexler et al 2004]] or Wexler et al 2005(([[http://www.liebertonline.com/doi/abs/10.1089/cmb.2005.12.928|Wexler, Y., Yakhini, Z., Kashi, Y., and Geiger, D. (2005). Finding approximate tandem repeats in genomic sequences. Journal of Computational Biology 12, 928-942.]]))     | ?     | Heuristic     | 1) Alignment parameters (match, mismatch, gap, terminal gap) 2) Maximum motif length 3) Similarity level between adjacent copies 4) Average similarity level between adjacent copies 5) Minimum alignment score with a repeating copy.     | One sequence, no limit in length.     | ?     | Yes     | no     | [[http://bioinfo.cs.technion.ac.il/atrhunter/|Yes]]     | Command-line [[http://bioinfo.cs.technion.ac.il/atrhunter/ATRinformation.htm|Download]]     | ?     | ?     | ?     | ?     | ?     |     |
+^ATRHunter      | 2004     | Not updated on a regular basis.     | [[http://scholar.google.ca/scholar?cites=11187065548778505423&as_sdt=2005&sciodt=0,5&hl=fr|47]]     | [[http://bioinfo.cs.technion.ac.il/atrhunter/ATR.pdf|Wexler et al 2004]] or Wexler et al 2005(([[http://www.liebertonline.com/doi/abs/10.1089/cmb.2005.12.928|Wexler, Y., Yakhini, Z., Kashi, Y., and Geiger, D. (2005). Finding approximate tandem repeats in genomic sequences. Journal of Computational Biology 12, 928-942.]]))     | ?     | Heuristic     | 1) Alignment parameters (match, mismatch, gap, terminal gap) 2) Maximum motif length 3) Similarity level between adjacent copies 4) Average similarity level between adjacent copies 5) Minimum alignment score with a repeating copy.     | One sequence, no limit in length.     | ?     | Yes     | no     | [[http://bioinfo.cs.technion.ac.il/atrhunter/|Yes]]     | Command-line [[http://bioinfo.cs.technion.ac.il/atrhunter/ATRinformation.htm|Download]]     | ?     | ?     | ?     | ?     | ?     |     |
 ^[[http://pgrc-35.ipk-gatersleben.de/portal/page/portal/PG_BICGH/P_BICGH/P_BICGH_TOOLS/P_BICGH_ITOOLS_MISA|MISA]]     | 2003     | 2010     | [[http://scholar.google.ca/scholar?cites=17518492932948765286&as_sdt=2005&sciodt=0,5&hl=fr|468]]     | Thiel et al 2003(([[http://www.springerlink.com/content/mv768txyrmxm4kga/|Thiel, Michalek, Varshney, and Graner (2003). Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (//Hordeum vulgare// L.). TAG Theoretical and Applied Genetics 106, 411-422.]]))     | One to six bp motifs     | ?     | Unit sizes; lower threshold of repeats for that specific unit; maximal number of bases between two adjacent microsatellites to be recognised as being a compound microsatellite     | Individual or group of sequences in fasta format     | Two files: one table file with localization and type of identified microsatellite(s); one file with statistics (e.g. frequency of a specific microsatellite type)     | Yes, compound and imperfect (but no indels) (other source mention it recognizes only perfect)     | Yes, with Primer3     | No     | Command-line [[http://pgrc.ipk-gatersleben.de/misa/misa.html|Download]]     | Platform independent     | perl script     | ?     | ?     | Detection of interrupted TR not efficient; inappropriate classification of different motifs; automated statistical analysis files not generated.     |     |
-^Mreps     | 2003     | ?     | [[http://scholar.google.ca/scholar?cites=7808444266556719865&as_sdt=2005&sciodt=0,5&hl=fr|156]]     | Kolpakov et al 2003(([[http://www.nar.oupjournals.org/cgi/doi/10.1093/nar/gkg617|Kolpakov, R., Bana, G., and Kucherov, G. (2003). mreps: efficient and flexible detection of tandem repeats in DNA. Nucleic Acids Research 31, 3672-3678.]]))     | ?     | Mixed combinatorial/heuristic paradigm     | Start and end positions of the region to be processed; length interval, period interval, minimal exponent of the repetitions to report; resolution level, use or not of the sliding window.     | One file with multiple sequences in the fasta format.     | list of all repeats, with start and end positions of the repeat in the sequence, overall size of the repeat, period, exponent, error level, the repeat sequence itself     | Yes, imperfect and compound (not indels)     | Yes     | [[http://bioinfo.lifl.fr/mreps/mreps.php|Yes]] (or [[http://mobyle.pasteur.fr/cgi-bin/portal.py?#forms::mreps|here]])     | Command-line [[http://bioinfo.lifl.fr/mreps//|Download]]     | Linux, SunOS, Digital Unix and Windows systems. Online?     | ANSI C     | Should be fast. linear in the sequence length     | ?     | Automated statistical analysis files not generated;     |     |
+^Mreps     | 2003     | ?     | [[http://scholar.google.ca/scholar?cites=7808444266556719865&as_sdt=2005&sciodt=0,5&hl=fr|156]]     | Kolpakov et al 2003(([[http://www.nar.oupjournals.org/cgi/doi/10.1093/nar/gkg617|Kolpakov, R., Bana, G., and Kucherov, G. (2003). mreps: efficient and flexible detection of tandem repeats in DNA. Nucleic Acids Research 31, 3672-3678.]]))     | Sites shorter than period + 9 are automatically discarded.     | Mixed combinatorial/heuristic paradigm     | Start and end positions of the region to be processed; length interval, period interval, minimal exponent of the repetitions to report; resolution level, use or not of the sliding window.     | One file with multiple sequences in the fasta format.     | list of all repeats, with start and end positions of the repeat in the sequence, overall size of the repeat, period, exponent, error level, the repeat sequence itself     | Yes, imperfect and compound (not indels)     | Yes     | [[http://bioinfo.lifl.fr/mreps/mreps.php|Yes]] (or [[http://mobyle.pasteur.fr/cgi-bin/portal.py?#forms::mreps|here]])     | Command-line [[http://bioinfo.lifl.fr/mreps//|Download]]     | Linux, SunOS, Digital Unix and Windows systems. Online?     | ANSI C     | Should be fast. linear in the sequence length     | ?     | Automated statistical analysis files not generated;     |     |
 ^STRING      | 2003     | 2003     | [[http://scholar.google.ca/scholar?cites=7212951020758895252&as_sdt=2005&sciodt=0,5&hl=fr|32]]     | Parisi et al 2003(([[http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/btg268|Parisi, V., De Fonzo, V., and Aluffi-Pentini, F. (2003). STRING: finding tandem repeats in DNA sequences. Bioinformatics 19, 1733-1738.]]))     | No limit in repeat length     | Heuristic; dynamic programming procedure.     | ?     | One file with one sequence, no limit in length.     | Length of the consensus word; first and last position of the TR; number of repeated units; score; consensus word; flanking sequences; alignment between the model TR and the given sequence; number of indels; number of matches and mismatches; TR base composition percentages; flag indicating a likely nested expansion.     | Yes, imperfect and compound (and indels?)     | No but may be possible     | A web interface is mentioned in the original publication, but cannot be found     | Command-line [[http://www.caspur.it/~castri/STRING/|Download]]     | Unix, Windows, MacOS     | C     | Slowly increases as a function of the sequence length, while it increases more quickly as a function of the number of TRs.     | ?     | Automated statistical analysis files not generated.     |     |
-^W-SSRF     | 2003     | ?     | [[http://scholar.google.ca/scholar?cites=6592174860693683120&as_sdt=2005&sciodt=0,5&hl=fr|8]]     | Sreenu et al 2003(([[http://www.ncbi.nlm.nih.gov/pubmed/15130803|Sreenu, V. B., Ranjitkumar, G., Swaminathan, S., Priya, S., Bose, B., Pavan, M. N., Thanu, G., Nagaraju, J., and Nagarajaram, H. A. (2003). MICAS: a fully automated web server for microsatellite extraction and analysis from prokaryote and viral genomic sequences. Appl. Bioinformatics 2, 165-168.]]))     | 1 to 10 bp long     | Scans a nucleotide sequence     | ?     | One file with one sequence. Upload limit is a 20 kb file.      | Sequence content of the motif, repeat numbers, start and end position of the tract in the sequence     | No, perfect only     | Yes, using Autoprimer (in MICAS)     | No     | The user friendly GUI (graphical user interface) is MICAS, Available upon request to the [[mailto:[email protected]|authors]]     | MICAS is [[http://210.212.212.7/MIC/index.html|web-only]]     | Java     | ?     | ?     | ?     |     |
+^W-SSRF     | 2003     | ?     | [[http://scholar.google.ca/scholar?cites=6592174860693683120&as_sdt=2005&sciodt=0,5&hl=fr|8]]     | Sreenu et al 2003(([[http://www.ncbi.nlm.nih.gov/pubmed/15130803|Sreenu, V. B., Ranjitkumar, G., Swaminathan, S., Priya, S., Bose, B., Pavan, M. N., Thanu, G., Nagaraju, J., and Nagarajaram, H. A. (2003). MICAS: a fully automated web server for microsatellite extraction and analysis from prokaryote and viral genomic sequences. Appl. Bioinformatics 2, 165-168.]]))     | 1 to 10 bp long     | Scans a nucleotide sequence     | ?     | One file with one sequence. Upload limit is a 20 kb file.      | Sequence content of the motif, repeat numbers, start and end position of the tract in the sequence     | No, perfect only     | Yes, using Autoprimer (in MICAS)     | No     | The user friendly GUI (graphical user interface) is MICAS, Available upon request to the [[mailto:[email protected]|authors]]     | MICAS is [[http://micas.cdfd.org.in:8080/MIC/|web-only]]     | Java     | ?     | ?     | ?     |     |
 ^IRF program     | 2004     | 2007     | [[http://scholar.google.ca/scholar?cites=7789233353140150696&as_sdt=2005&sciodt=0,5&hl=fr|80]]     | Warburton et al 2004(([[http://www.genome.org/cgi/doi/10.1101/gr.2542904|Warburton, P. E. (2004). Inverted repeat structure of the human genome: The X-chromosome contains a preponderance of large, highly homologous inverted repeats that contain testes genes. Genome Research 14, 1861-1869.]]))     | ?     | ?     | ?     | ?     | ?     |      |      | ?     | Command-line [[http://tandem.bu.edu/news.html#mar2007|Download]]     | ?     | ?     | ?     | ?     | ?     |     |
 ^ExTRS     | 2004     | ?     | [[http://scholar.google.ca/scholar?cites=10980601425678591553&as_sdt=2005&sciodt=0,5&hl=fr|33]]     | Krishnan and Tang 2004(([[http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/bth311|Krishnan, A., and Tang, F. (2004). Exhaustive whole-genome tandem repeats search. Bioinformatics 20, 2702-2710.]]))     | ?     | Exhaustive     | ?     | One file with one sequence, no limit in length.     | Redundancy in the output is reduced     | Yes, substitutions (not indels)     |      | ?     | ? Available upon request to the [[mailto:[email protected]|authors]]     | ?     | Source code available only on request     | Near-proportional to the number of TR found     | ?     | ?     |     |
-^SRF     | 2004     | ?     | [[http://scholar.google.ca/scholar?cites=7521918802336115515&as_sdt=5&sciodt=0&hl=fr|54]]     | Sharma et al. 2004(([[http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/bth103|Sharma, D., Issac, B., Raghava, G. P. S., and Ramaswamy, R. (2004). Spectral Repeat Finder (SRF): identification of repetitive sequences using Fourier transformation. Bioinformatics 20, 1405-1412.]]))     | ?     | Spectral technique     | Minimum repeat length;  maximum repeat length; minimum % Match; FFT peakccut-off; (optional) Minimum Number of Copies.     | One file with one sequence, no limit in length. In fasta or genbank format.     | Information about the repeat unit, consensus pattern, region, copy number and score; as well as Fourier spectrum and the detailed analysis of any particular repeat unit.     | Yes, imperfect and indels     | No     | [[http://www.imtech.res.in/raghava/srf/submit.html|Yes]]     | ? Availability unknown, contact the [[mailto:[email protected]|author]]     | ?     | ?     | ?     | Repeats need not to be in tandem     | ?     |     |
+^SRF     | 2004     | 2004     | [[http://scholar.google.ca/scholar?cites=7521918802336115515&as_sdt=5&sciodt=0&hl=fr|55]]     | Sharma et al. 2004(([[http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/bth103|Sharma, D., Issac, B., Raghava, G. P. S., and Ramaswamy, R. (2004). Spectral Repeat Finder (SRF): identification of repetitive sequences using Fourier transformation. Bioinformatics 20, 1405-1412.]]))     | 2-300 bp (default is 2-10 bp)     | Spectral technique     | Minimum repeat length; Maximum repeat length; Minimum % Match; FFT peak cut-off; (optional) Minimum number of copies.     | One file with one sequence, no limit in length. In fasta or genbank format.     | Information about the repeat unit, consensus pattern, region, copy number and score; as well as Fourier spectrum and the detailed analysis of any particular repeat unit.     | Yes, imperfect and indels     | No     | [[http://www.imtech.res.in/raghava/srf/submit.html|Yes]]     | Available upon request to the [[mailto:[email protected]|author]]     | Linux and Mac     | Perl     | Execution time increases as a function of repeat/sequence length     | Repeats can be tandem, dispersed and/or imperfect     | ?     |     |
-^STAR     | 2004     | ?     | [[http://scholar.google.ca/scholar?cites=6796575892001734157&as_sdt=2005&sciodt=0,5&hl=fr|52]]     | Delgrange and Rivals 2004(([[http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/bth335|Delgrange, O., and Rivals, E. (2004). STAR: an algorithm to search for tandem approximate repeats. Bioinformatics 20, 2812-2820.]]))      | Only searches for predefined motifs >2 bp, but allows approximate repeats.     | Exhaustive     | DNA motif to search for; Position offset     | One file with one sequence     | ?     | Yes, only substitutions (not indels)     |      | [[http://www.atgc-montpellier.fr/star/|Yes]]     | Command-line [[http://www.atgc-montpellier.fr/star/binaries.php|Download]]     | Linux, SunOS, Mac OSX, and Windows systems.     | Source code not available     | Slow. The overall time complexity needed by STAR to find all ATR of a given motif of length p, in a sequence of length n, is O(np+n log n)     | ?     | Automated statistical analysis files not generated     |     |
+^STAR     | 2004     | ?     | [[http://scholar.google.ca/scholar?cites=6796575892001734157&as_sdt=2005&sciodt=0,5&hl=fr|52]]     | Delgrange and Rivals 2004(([[http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/bth335|Delgrange, O., and Rivals, E. (2004). STAR: an algorithm to search for tandem approximate repeats. Bioinformatics 20, 2812-2820.]]))      | Only searches for predefined motifs >2 bp, but allows approximate repeats.     | Exhaustive. As searching for microsatellites is a special cases of approximate TR, it can be done globally in a single run using the MotifFile parameter.  Contact the [[http://www.lirmm.fr/~rivals/|authors]] for more informations.     | File with one motif per line, and then each motif is searched independently. Position offset     | One file with one sequence     | ?     | Yes, substitutions and indels     |      | As a service on an [[http://www.atgc-montpellier.fr/star/|online platform]]     | Command-line [[http://www.atgc-montpellier.fr/star/binaries.php|Download]]     | Linux, SunOS, Mac OSX, and Windows systems.     | Source code not available     | Slow. The overall time complexity needed by STAR to find all ATR of a given motif of length p, in a sequence of length n, is O(np+n log n)     | Does not detect TR that would appear in a random sequence (false positives)     |      |     |
 ^TRA     | 2004     | 2004     | [[http://scholar.google.ca/scholar?cites=13056073161710952438&as_sdt=5&sciodt=0&hl=fr|21]]     | Bilgen et al 2004(([[http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/bth410|Bilgen, M., Karaca, M., Onus, A. N., and Ince, A. G. (2004). A software program combining sequence motif searches with keywords for finding repeats containing DNA sequences. Bioinformatics 20, 3379-3386.]]))     | ?     | Heuristic     | ?     | Multiple files with multiple sequences each (Max 1 Mb sequence) from ESTs.     | ?     | Yes, searches for exact–inexact TRs and exact–inexact compound repeats     | No?     | ?     | ? [[ftp://ftp.akdeniz.edu.tr/Araclar/TRA/|Download]]     | Windows     | C++ (with Microsoft Visual C++)     | ?     | Searches among the organisms, organs, tissue types and development stages     | ?     |     |
 ^MsatFinder     | 2005     | 2007     | 48     | Thurston and Field 2005(([[http://www.genomics.ceh.ac.uk/msatfinder/|Thurston, M. I., and Field, D. (2006). Msatfinder, (Oxford, UK: Centre for Ecology and Hydrology. Computer program)]]))     | One to 6 bp long     | ?     | 1) length of repeat 2) number repeat unit in the site 3) search engine (regex, multipass or iterative search)     | Limit of 10 Mb of sequence in the online access. Accepts GenBank, EMBL, Swissprot, FASTA, ASCII.     | Repeats, GFF, Counts, Msat_tabs, Flank_tabs, Fasta, MINE, Primers     | No, but detects compound perfect repeats     |      | [[http://www.genomics.ceh.ac.uk/cgi-bin/msatfinder/msatfinder.cgi|Yes]]     | Command-line [[http://www.genomics.ceh.ac.uk/msatfinder/#download|Download]]     | Unix (may work on Mac OSX)     | perl script     | ?     | Nucleic acid or amino acid sequence     | ?     |     |
-^Fireusat     | 2006     | ?     | [[http://scholar.google.ca/scholar?cites=17060705618169575807&as_sdt=2005&sciodt=0,5&hl=fr|5]] and [[http://scholar.google.ca/scholar?cites=66353776030260478&as_sdt=5&sciodt=0&hl=fr|this]]     | de Riddera at al 2006(([[http://portal.acm.org/citation.cfm?doid=1216262.1216289|de Riddera, C., Kourie, D. G., and Watson, B. W. (2006). FireμSat. In Proceedings of the 2006 annual research conference of the South African institute of computer scientists and information technologists on IT research in developing couuntries  - SAICSIT  ’06 (Somerset West, South Africa), pp. 247-256.]]))     | Length set by the user, usually > 2 bp long     | Uses regular expressions and ?     | Minimum and maximum length of motif; maximum allowable motif error; maximum allowable substring error; penalty values for calculating substring error; maximum allowable number of approximate TR that may occur consecutively; the minimum number of elements (microsatellites) of a TR.     | One file with one sequence     | ?     | Yes, substitutions and indels     | No     | No     | ? Availability unknown, contact the [[mailto: driddc@unisa.ac.za;[email protected].ac.za;[email protected].za|authors]]     | ?     | ?     | ?     | Designed for microsatellites, but can detect any type of TR     | ?     |     |
+^FireµSat     | 2006     | 2011     | [[http://scholar.google.ca/scholar?cites=17060705618169575807&as_sdt=2005&sciodt=0,5&hl=fr|5]] and [[http://scholar.google.ca/scholar?cites=66353776030260478&as_sdt=5&sciodt=0&hl=fr|this]]     | de Ridder at al 2006(([[http://portal.acm.org/citation.cfm?doid=1216262.1216289|de Riddera, C., Kourie, D. G., and Watson, B. W. (2006). FireµSat. In Proceedings of the 2006 annual research conference of the South African institute of computer scientists and information technologists on IT research in developing countries  - SAICSIT  ’06 (Somerset West, South Africa), pp. 247-256.]])) and de Ridder at al 2013(([[http://www.sciencedirect.com/science/article/pii/S1570866712001657|De Ridder, C., D.G. Kourie, B.W. Watson, T.R. Fourie, and P.V. Reyneke (2013). Fine-tuning the search for microsatellites. Journal of Discrete Algorithms 20: 21–37.]]))     | 1 to 5 bp. Length set by the user. The next update should allow for detection of 6 to 100 bp repeats.     | Uses Counting Finite Automata (which are regular language acceptors)     | Max Motif Error (per motif); Max adjacent ATR elements; Motif Range Options; Min required TR elements; Max substring error (a threshold); Mismatch penalty (m_p); Delete penalty (d_p); Insert penalty (i_p).     | One fasta file with one sequence     | File in .csv format.     | Yes, substitutions and indels, but not compound loci.     | No     | No     | GUI and command-line, [[http://www.dna-algo.co.za/|Download]]     | Windows; Linux in progress     | C++ and MatLab     | Run time increases linearly with the sequence length; does not increase with longer motif lengths.     | Designed for microsatellites, but can detect any type of TR     | Fast, simple and flexible.     |     |
-^Phobos     | 2006     | 2010     | ?     | Mayer 2010(([[http://www.ruhr-uni-bochum.de/spezzoo/cm/cm_phobos.htm |Mayer, C. (2010). Phobos: Highly accurate search for perfect and imperfect tandem repeats in complete genomes by Christoph Mayer, (Bochum, Germany: Ruhr-Universität Bochum,Faculty of Biological Sciences and Biotechnology). Computer program.]]))      | Perfect (and imperfect?) satellites with a pattern size of 1 - 10000 bp (?)     | Uses alignment scores     | ?     | One file with multiple sequence with no limit in sequence length.     | ?     | Yes. Searches for imperfect satellites  in the pattern size range 1 - 50 bp; the site can be up to 5000 bp long     | No     | No     | User friendly GUI (graphical user interface); and easily scriptable Command-line program [[http://www.ruhr-uni-bochum.de/spezzoo/cm/cm_phobos.htm|Download]]     | ?     | ?     | ?     | Implemented in STAMP and Geneious     | ?     |     |
+^Phobos     | 2006     | 2010     | ?     | Mayer 2010(([[http://www.ruhr-uni-bochum.de/spezzoo/cm/cm_phobos.htm |Mayer, C. (2010). Phobos: Highly accurate search for perfect and imperfect tandem repeats in complete genomes by Christoph Mayer, (Bochum, Germany: Ruhr-Universität Bochum,Faculty of Biological Sciences and Biotechnology). Computer program.]]))      | Perfect and imperfect TR, with a pattern size of 1 - 10 000 bp     | Exhaustive, uses alignment scores     | Mismatch score, indel score, minimum score, minimum length, minimum perfection, and others.     | One file in fasta format, with multiple sequence. No limit in sequence length.     | Text file, different formats, including gff and fasta     | Yes. Substitutions and indels.      | Not in itself, but yes as implemented in STAMP or Geneious.      | No     | User friendly GUI and easily scriptable Command-line program [[http://www.ruhr-uni-bochum.de/ecoevo/cm/cm_phobos.htm|Download]]     | MacOSX, Linux, Windows.     | C++     | Execution time increases with pattern size range. Very fast in the size range 1-10 bp, slow for patterns in the size range above 10-20 bp.     | Can be incorporated into pipelines. Implemented in STAMP and Geneious.     | Free only for academic users.     |     |
 ^SSRscanner     | 2006     | ?     |  [[http://scholar.google.ca/scholar?cites=15246530144073441813&as_sdt=2005&sciodt=0,5&hl=fr|3]]     | Anwar and Khan 2006(([[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891659/|Anwar, T., and Khan, A. (2006). SSRscanner: a program for reporting distribution and exact location of simple sequence repeats. Bioinformation 1, 89-91.]]))     | Only searches for predefined motifs     | Exhaustive, uses dictionary approach.     | File containing motifs of different repeat types; number of times for the motifs to be repeated     | One file with one sequence     | Motifposition.txt (gives the frequency of each repeat provided in the motif file) and (2) Motifresult.exe (gives the specific location of each repeat)     | No, perfect only     | No     | No     | Command-line Availability unknown, contact the [[mailto:[email protected]|author]]     | Platform independent     | perl script     | ?     | ?     | ?     |     |
 ^TandemSWAN     | 2006     | 2006     | [[http://scholar.google.ca/scholar?cites=9674288721814272003&as_sdt=2005&sciodt=0,5&hl=fr|35]]     | Boeva et al 2006(([[http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/btk032|Boeva, V., Regnier, M., Papatsenko, D., and Makeev, V. (2006). Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression. Bioinformatics 22, 676-684.]]))     | Fuzzy TR (degenerate TR without indels, but with a high substitution rate), > 3 bp long     | Heuristic     | Degeneracy level; the minimal and the maximal period sizes; the mode of statistical significance calculation (i.e. the "motif" mode or the "mask" mode); in plain, fasta, EMBL or GenBank format.     | One file with one sequence, no limit in length. In plain, EMBL, fasta or GenBank format.     | A file with: the start, end, and length of TR; motif size (period); the number of copies; the motif consensus sequence; the number of words in the motif that satisfy the consensus; the probability, P-value and statistical significance for the "motif" and the "mask"; the TR itself.     | Yes, only imperfect (no indels)     | No     | [[http://favorov.imb.ac.ru/swan/form_TS.html?web_form=Query+the+new+version+of+TandemSWAN+web+form+now!|Yes]]     | Command-line [[http://favorov.imb.ac.ru/swan/|Download]]     | Platform independent     | C     | ?     | Can simultaneously identify both short- and large period repeats with approximately the same fuzziness     | ?     |     |
@@ Line 38: / Line 38: @@
 ^SciRoKo     | 2007     | 2008     | [[http://scholar.google.ca/scholar?cites=16996584693111364287&as_sdt=2005&sciodt=0,5&hl=fr|44]]     | Kofler et al 2007(([[http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/btm157|Kofler, R., Schlotterer, C., and Lelley, T. (2007). SciRoKo: a new tool for whole genome microsatellite search and investigation. Bioinformatics 23, 1683-1685.]]))     | One to 6 bp long     | ?     | Hits (identity with a virtual perfect microsatellite), number of mismatches (mm), mismatch penalty (mmP) and the length of the SSR motif (mL).     | One file with multiple sequences in the fasta format.     | ?     | Yes, imperfect and compound (indels?)     |      | No     | User friendly GUI (graphical user interface) standalone. [[http://www.kofler.or.at/bioinformatics/SciRoKo/index.html|Download]]     | Windows. Should be platform independent, but Mac users have not been able install     | C#     | Fast     | ?     | Depends on .NET framework     |     |
 ^Msatcommander     | 2008     | 2011     | [[http://scholar.google.ca/scholar?cites=3185583603820687905&as_sdt=2005&sciodt=0,5&hl=fr|102]]     | Faircloth 2008(([[http://doi.wiley.com/10.1111/j.1471-8286.2007.01884.x|Faircloth, B. C. (2008). msatcommander: detection of microsatellite repeat arrays and automated, locus-specific primer design. Molecular Ecology Resources 8, 92-94.]]))     | ?     | Uses regular expressions     | ?     | One file with multiple sequences in the fasta format.     | Either a summary file (array detection only) or a directory at a user-selectable location     | No, but accepts N     | Yes, with Primer3, includes 5'-tailing     | No     | User friendly GUI (graphical user interface) standalone. [[http://code.google.com/p/msatcommander/|Download]]     | MacOS X, Windows, Unix.     | Python     | ?     | Rapid and automated microsatellite array detection, locus-specific primer design, and 5'-tailing of designed primers     | ?     |     |
-^ReRep     | 2008     | 2008     | [[http://scholar.google.ca/scholar?cites=255635357253003447&as_sdt=2005&sciodt=0,5&hl=fr|5]]     | Otto et al 2008(([[http://www.biomedcentral.com/1471-2105/9/366|Otto, T. D., Gomes, L. H. F., Alves-Ferreira, M., de Miranda, A. B., and Degrave, W. M. (2008). ReRep: Computational detection of repetitive sequences in genome survey sequences (GSS). BMC Bioinformatics 9, 366.]]))     | ?     | Uses self-similarity searches     | ?     | Genome survey sequences(GSS) files, including 454-reads     | ?     | Yes, substitutions and indels     | No     | No     | Command-line [[http://bioinfo.pdtis.fiocruz.br/ReRep/|Download]]     | Linux     | Perl     | ?     | Can detect de novo repeats in Genome Sequence Survey sequence data     | ?    |
+^ReRep     | 2008     | 2008     | [[http://scholar.google.ca/scholar?cites=255635357253003447&as_sdt=2005&sciodt=0,5&hl=fr|5]]     | Otto et al 2008(([[http://www.biomedcentral.com/1471-2105/9/366|Otto, T. D., Gomes, L. H. F., Alves-Ferreira, M., de Miranda, A. B., and Degrave, W. M. (2008). ReRep: Computational detection of repetitive sequences in genome survey sequences (GSS). BMC Bioinformatics 9, 366.]]))     | ?     | Uses self-similarity searches     | ?     | Genome survey sequences(GSS) files, including 454-reads     | ?     | Yes, substitutions and indels     | No     | No     | Command-line [[http://www.dbbm.fiocruz.br/labwim/bioinfoteam/index.pl?action=services|Download]]     | Linux     | Perl     | ?     | Can detect de novo repeats in Genome Sequence Survey sequence data     | ?    |
-^t-REKS     | 2009     | ?     | [[http://scholar.google.ca/scholar?cites=208721574341442296&as_sdt=2005&sciodt=0,5&hl=fr|5]]     | Jorda and Kajava 2009(([[http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/btp482|Jorda, J., and Kajava, A. V. (2009). T-REKS: identification of Tandem REpeats in sequences with a K-meanS based algorithm. Bioinformatics 25, 2632-2638.]]))     | ?     |  Uses K-means algorithm     | delta-l Allowed % of length variability, P*sim—similarity threshold and an option to allow or not  the detection of overlaping TR.     | ?     | Output placed in a database accessible online     | Yes, substitutions (indels?)     | No     | [[http://bioinfo.montp.cnrs.fr/?r=t-reks|Yes]]     | User friendly GUI (graphical user interface) standalone. [[http://bioinfo.montp.cnrs.fr/?r=t-reks|Download]]     | ?     | Java     | ?     | Nucleic acid or amino acid sequence     | ?    |
+^T-REKS     | 2009     | ?     | [[http://scholar.google.ca/scholar?cites=208721574341442296&as_sdt=2005&sciodt=0,5&hl=fr|5]]     | Jorda and Kajava 2009(([[http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/btp482|Jorda, J., and Kajava, A. V. (2009). T-REKS: identification of Tandem REpeats in sequences with a K-meanS based algorithm. Bioinformatics 25, 2632-2638.]]))     | No limits in repeat length     | Short string extension and K-means algorithm.     | delta-l Allowed % of length variability, P*sim—similarity threshold and an option to allow or not  the detection of overlaping TR.     | Sequences in FASTA format.     | Output with start, end, length of TR and multiple alignment of the repeats.     | Yes, substitutions and indels.     | No     | [[http://bioinfo.montp.cnrs.fr/?r=t-reks|Yes]]     | User friendly GUI (graphical user interface) standalone. [[http://bioinfo.montp.cnrs.fr/?r=t-reks|Download]]     | Platform independent     | Java     | Fast. Execution time is linear (directly proportional) to the sequence length.     | Can be applied to nucleic acid, amino acid or any text sequence.     | ?    |
 ^BwTRS     | 2010     | 2009     | [[http://scholar.google.ca/scholar?cites=7603849771779688492&as_sdt=2005&sciodt=0,5&hl=fr|2]]     | Pokrzywa and Polanski 2010(([[http://linkinghub.elsevier.com/retrieve/pii/S0888754310001758|Pokrzywa, R., and Polanski, A. (2010). BWtrs: A tool for searching for tandem repeats in DNA sequences based on the Burrows–Wheeler transform. Genomics 96, 316-321.]]))     | ?     | Exhaustive; uses efficient data compression algorithm     | "Minimum motif size", "Maximum motif size", "Minimum repeat size" and "Minimum repeat ratio".     | One file with multiple sequences in the fasta format; or GenBank id. Accepts nucleotides and amino acids sequences.     | List of all TR with: Start and End (position of the TR in the sequence); Motif length; Ratio (between the motif length and the consensus repeat length); the motif itself. HTML or text.     | No     | No     | [[http://bwtools.polsl.pl/BWtrs/input.jsp|Yes]], runs on a standard Tomcat servlet container without any local database     | ? Availability unknown, contact the [[mailto: [email protected]|authors]].     | ?     | Java     | Depends on sequence length     | Nucleic acid or amino acid sequence     | ?    |
-^QDD     | 2010     | 2011     | [[http://scholar.google.ca/scholar?cites=146872267015635519&as_sdt=5&sciodt=0&hl=fr|16]]     | Meglecz et al 2010(([[http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/btp670|Meglecz, E., Costedoat, C., Dubut, V., Gilles, A., Malausa, T., Pech, N., and Martin, J.-F. (2009). QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects. Bioinformatics 26, 403-404.]]))     | 2 to 6 bp motifs     | ?     | ?     | Multiple files with one sequence each, with raw sequence reads in fasta format.     | ?     |      | Yes     | No     | Command-line. Availability unknown, contact the [[mailto:[email protected]|authors]].     | Linux, Windows     | Perl script (with Bioperl)     | ?     | Sorts raw sequences by tag, removes adapters, detects TR sites, redundancy and mobile element, selects target microsatellites, and designs primer.      | ?    |
+^QDD, QDD2     | 2010     | 2011     | [[http://scholar.google.ca/scholar?cites=146872267015635519&as_sdt=5&sciodt=0&hl=fr|16]]     | Meglecz et al 2010(([[http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/btp670|Meglecz, E., Costedoat, C., Dubut, V., Gilles, A., Malausa, T., Pech, N., and Martin, J.-F. (2009). QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects. Bioinformatics 26, 403-404.]]))     | 2 to 6 bp motifs     | First step: detects all perfect TR with at least 5 repetitions as target. Later (step 3, primer design), TR of 3-4 repeats are also detected and blocks of repetitions are pooled into a complex microsatellite if the distance between them is not greater than the footprint of the longest motif of two neighbors.     | Not parametrable     | One fasta file with multiple short sequences (< ~2Mb). Multiple files can be run in batch.     | (a) Fasta file with sequences containing a perfect TR of at least 5 repeats. (b) Text file with sequence code and length, number of microsatellites, TR motif, first position, last position, and number of repeats. csv file with primer information.      | Yes if it contains at least 5 perfect repeats. Imperfect TR will be detected as composite site.     | Yes     | [[http://gsite.univ-provence.fr/gsite/Local/egee/dir/meglecz/QDD.html|Coming soon]]      | Command-line. Availability unknown, contact the [[mailto:[email protected]|authors]].     | Linux, Windows     | Perl script (with Bioperl)     | ?     | Sorts raw sequences by tag, removes adapters, detects TR sites, redundancy, selects target microsatellites, and designs primer. Detects contamination.      | ?    |
 ^TRStalker (in TReaDS)     | 2010     | ?     | [[http://scholar.google.ca/scholar?cites=10471014057375486653&as_sdt=5&sciodt=0&hl=fr|1]]     | Pellegrini et al 2010(([[http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/btq209|Pellegrini, M., Renda, M. E., and Vecchio, A. (2010). TRStalker: an efficient heuristic for finding fuzzy tandem repeats. Bioinformatics 26, i358-i366.]]))     | ?     | ?     | ?     | ?     | ?     | Yes, imperfect and indels     |      | [[http://yucca.iit.cnr.it:8080/treads/|Yes]]     | ? Availability unknown, contact the [[mailto:[email protected]|authors]]     | ?     | ?     | ?     | ?     | ?    |
 ^Pipeline name     ^ year released     ^ Latest update     ^ Number of citations     ^ Original publication     ^ Repeats detected     ^ Algorithm used     ^ Parameters     ^ Input file     ^ Output file     ^ Detect imperfect or compound loci     ^ Design primers     ^ Online access     ^ Interface (GUI or commandline)     ^ Platform     ^ language     ^ Speed     ^ Special Features     ^ Limitations    |
 ^repeatfinder     | 2001     | ?     | ?     | Volfovsky et al 2001(([[http://genomebiology.com/2001/2/8/research/0027|Volfovsky, N., Haas, B., and Salzberg, S. (2001). A clustering method for repeat analysis in DNA sequences. Genome Biology 2, research0027.1 - research0027.11.]]))     | ?     | Uses REPuter     | ?     | ?     | ?     | ?     | ?     | No     | Command-line [[http://www.cbcb.umd.edu/software/RepeatFinder/|Download]]     | Linux RedHat 6.x+, Sun Solaris, and Alpha OSF1     | ? Open Source     | ?     | ?     | ?    |
 ^MsatMiner     | 2005     | ?     |      | Thurston and Field 2005(([[http://www.genomics.ceh.ac.uk/msatminer/|Thurston, M. I. (2005). Msatminer - scripts for processing msatfinder output, (Oxford, UK: Centre for Ecology and Hydrology). Computer program.]]))     | ?     | Uses msatfinder for motif discovery     |      | Different format of sequence file     | More statistical analysis are possible.     | Yes, imperfect and compound (indels?)     | Possible when using additional scripts     | ?     | Command-line     | Unix and MacOS     | Collection of perl scripts     | ?     | ?     | Running scripts is possibly complicated    |
-^E-TRA     | 2005     | 2004     | [[http://scholar.google.ca/scholar?cites=6055835177193667419&as_sdt=5&sciodt=0&hl=fr|12]]     | Karaca et al 2005(([[Available at: http://www.springerlink.com/index/10.1007/BF02715889|Karaca, M., Bilgen, M., Onus, A. N., Ince, A. G., and Elmasulu, S. Y. (2005). Exact tandem repeats analyzer (E-TRA): A new program for DNA sequence mining. J Genet 84, 49-54.]]))     | 1 to 1000 bp repeat     | Uses TRA     | ?     | Multiple files with multiple sequences each (maximum of 1 Mb long)     |      | Yes, compound and imperfect     | Yes     | No     | user friendly GUI (graphical user interface) [[ftp://ftp.akdeniz.edu.tr/Araclar/TRA/|Download]]     | Windows     | C++ (with Microsoft Visual C++)     |      | Searches among the organisms, organs, tissue types and development stages     | Only 1 Mb of input sequence length    |
+^E-TRA     | 2005     | 2004     | [[http://scholar.google.ca/scholar?cites=6055835177193667419&as_sdt=5&sciodt=0&hl=fr|12]]     | Karaca et al 2005(([[http://www.springerlink.com/index/10.1007/BF02715889|Karaca, M., Bilgen, M., Onus, A. N., Ince, A. G., and Elmasulu, S. Y. (2005). Exact tandem repeats analyzer (E-TRA): A new program for DNA sequence mining. J Genet 84, 49-54.]]))     | 1 to 1000 bp repeat     | Uses TRA     | ?     | Multiple files with multiple sequences each (maximum of 1 Mb long)     |      | Yes, compound and imperfect     | Yes     | No     | user friendly GUI (graphical user interface) [[ftp://ftp.akdeniz.edu.tr/Araclar/TRA/|Download]]     | Windows     | C++ (with Microsoft Visual C++)     |      | Searches among the organisms, organs, tissue types and development stages     | Only 1 Mb of input sequence length    |
-^SSRprimer     | 2006     | ?     | 29     | Robinson et al. 2004(([[http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/bth104|Robinson, A. J., Love, C. G., Batley, J., Barker, G., and Edwards, D. (2004). Simple sequence repeat marker loci discovery using SSR primer. Bioinformatics 20, 1475-1476.]]))     | 2 to >6 bp long repeats     | Uses Sputnik     |      |      |      |      | Yes uses Primer3     | ?     | ?     | ?     | Perl scripts     | ?     | ?     | ?    |
+^SSRprimerII     | 2006     | 2009     | 29     | Robinson et al. 2004(([[http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/bth104|Robinson, A. J., Love, C. G., Batley, J., Barker, G., and Edwards, D. (2004). Simple sequence repeat marker loci discovery using SSR primer. Bioinformatics 20, 1475-1476.]])) and Jewell et al. 2006(([[http://www.nar.oxfordjournals.org/cgi/doi/10.1093/nar/gkl083|Jewell, E. et al. (2006). SSRPrimer and SSR Taxonomy Tree: Biome SSR discovery. Nucleic Acids Research 34, W656-W659.]]))     | 2 to >6 bp long repeats     | Uses Sputnik     |      | Limit of 4000 bp sequence     |      |      | Yes uses Primer3     | [[http://flora.acpfg.com.au/ssrprimer2/cgi-bin/index|Yes]]     | ? Contact the [[http://www.appliedbioinformatics.com.au/|group]]     | ?     | Perl scripts     | ?     | ?     | ?    |
-^TRAP     | 2006     | 2005     | 10     | Sobreira et al 2006(([[http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/bti809|Sobreira, T. J. P., Durham, A. M., and Gruber, A. (2005). TRAP: automated classification, quantification and annotation of tandemly repeated sequences. Bioinformatics 22, 361-362.]]))     | 1 to 2000 bp repeat   | Uses TRF     | All TRF parameters: minimum and maximum number of motifs, minimum and maximum motif size (period), minimum size of flanking regions and minimum match % between adjacent motifs.     | One file with multiple sequences in fasta format.     | Output files in many format (csv, HTML, flat files, and GFF)     |   Yes, imperfect and compound   |  no    | no     | Command-line [[http://www.coccidia.icb.usp.br/trap/trapRegister/|Download]]     | Unix     | Perl scripts     |  Near-proportional to the number of TR founded by TRF   | Selection, classification, quantification and automated annotation of TR sequences     |     |
+^TRAP     | 2006     | 2005     | 10     | Sobreira et al 2006(([[http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/bti809|Sobreira, T. J. P., Durham, A. M., and Gruber, A. (2005). TRAP: automated classification, quantification and annotation of tandemly repeated sequences. Bioinformatics 22, 361-362.]]))     | 1 to 2000 bp repeat   | Uses TRF     | All TRF parameters, as well as: min and max number of motifs; min and max motif size (period), min size of flanking regions and min match % between adjacent motifs.     | One file with multiple sequences in fasta format.     | Many formats (csv, HTML, flat files, and GFF)     |   Yes, imperfect and compound   |  No, but generates a fasta file with TR regions masked with Ns    | no     | Command-line [[http://www.coccidia.icb.usp.br/trap/trapRegister/|Download]]     | Unix; MacOSX     | Perl scripts     |  Near-proportional to the number of TRs found by TRF   | Selection, classification, quantification and automated annotation of TR sequences     | Not compatible with MS Windows version of TRF     |
 ^cid     | 2008     | ?     | 11     | Freita et al 2008(([[http://doi.wiley.com/10.1111/j.1471-8286.2007.01950.x|Freitas, P. D., Martins, D. S., and Galetti, P. M. (2008). cid: a rapid and efficient bioinformatic tool for the detection of SSRs from genomic libraries. Molecular Ecology Resources 8, 107-108.]]))     | Same as MISA     | Uses MISA for tandem repeat detection, and other external programs for other steps     |      | Set of chromatograms or multiFASTA file     | List of useful primers     |      | Yes, using Primer3     | ?     | Web environment, Availability unknown, contact the [[mailto: [email protected]|authors]]     | ?     | perl and php to connect the different tools     | ?     | Can mask vectors and adaptors regions of cloned sequences     | ?    |
 ^Etandem (in EMBOSS)     | 2008     | ?     | [[http://scholar.google.ca/scholar?cites=2718801218157611554&as_sdt=2005&sciodt=0,5&hl=fr|2119]]     | Rice et al 2010(([[http://linkinghub.elsevier.com/retrieve/pii/S0168952500020242|Rice, P., Longden, I., and Bleasby, A. (2000). EMBOSS: The European Molecular Biology Open Software Suite. Trends in Genetics 16, 276-277.]]))     | ?     | ?     | ?     | ?     | ?     | ?     | ?     | ?     | ?     | ?     | ?     | ?     | ?     | ?    |
-^STAMP     | 2009     | ?     | [[http://scholar.google.ca/scholar?cites=595056583974417882&as_sdt=2005&sciodt=0,5&hl=fr|16]]"     | Kraemer et al 2009(([[http://www.biomedcentral.com/1471-2105/10/41|Kraemer, L., Beszteri, B., Gäbler-Schwarz, S., Held, C., Leese, F., Mayer, C., Pöhlmann, K., and Frickenhaus, S. (2009). STAMP: Extensions to the STADEN sequence analysis package for high throughput interactive microsatellite marker design. BMC Bioinformatics 10, 41.]]))     | ?     | Based on STADEN, uses non-probabilistic Phobos algorithm to detect all TR that match user-defined options. TROLL was previously in STADEN, but cannot detect imperfect motifs.     | ?     | ?     | ?     | Yes (?), but only those defined by user.     | Yes, including for multiplexing microsatellites markers. Integrates Primer3 into GAP4     | No     | Command-line [[http://www.awi.de/en/research/scientific_computing/research_topics/bioinformatics/software/#c6699|Download]]     | Platform independent     | tcl     | ?     | ?     | ?    |
+^STAMP     | 2009     | 2010     | [[http://scholar.google.ca/scholar?cites=595056583974417882&as_sdt=2005&sciodt=0,5&hl=fr|16]]     | Kraemer et al 2009(([[http://www.biomedcentral.com/1471-2105/10/41|Kraemer, L., Beszteri, B., Gäbler-Schwarz, S., Held, C., Leese, F., Mayer, C., Pöhlmann, K., and Frickenhaus, S. (2009). STAMP: Extensions to the STADEN sequence analysis package for high throughput interactive microsatellite marker design. BMC Bioinformatics 10, 41.]]))     | Imperfect and perfect, 1-unlimited     | Based on STADEN, uses Phobos (exhaustive search) to detect all TR that match user-defined options. TROLL was previously in STADEN.     | Mismatch score, indel score, minimum score, minimum length, minimum perfection, and others.     | Fasta file with one or multiple sequences and no limit in sequence length, Staden experimental files.     | Text files, different formats     | Yes (substitutions and indels), but only those defined by user.     | Yes, also for multiplexing microsatellites markers. Integrates Primer3 into GAP4     | No     | Plugged into the GUI offered by STADEN, [[http://www.awi.de/en/research/scientific_computing/research_topics/bioinformatics/software/#c6699|Download]]     | Mac Os X, Linux, Windows. Others upon request.     | TCL, C++     | Execution time increases with pattern size range. Very fast in the size range 1-10 bp, slow for patterns in the size range above 20 bp     | Automatic pipeline, interaction in primer design step possible.     | Free only for academic users.    |
 ^WebSat     | 2009     | ?     | [[http://scholar.google.ca/scholar?cites=16509104044085592718&as_sdt=5&sciodt=0&hl=fr|22]]     | Martins et al 2009(([[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2646864/|Martins, W. S., Soares Lucas, D., de Souza Neves, K. F., and Bertioli, D. J. (2009). WebSat ‐ A web software for microsatellite marker development. Bioinformation 3, 282-283.]]))     | Same as TROLL     | Uses TROLL     | Motif length and minimum number of motifs     | Individual sequences, in raw or FASTA format, or a group of sequences in a multi-FASTA format, maximum of 150 000 characters.     | ?     | ?     | ?     | [[http://wsmartins.net/websat/|Yes]] Uses Ajax techniques     | Command-line [[http://sourceforge.net/projects/satfinder/|Download]]     | ?     | Written in PHP and JavaScript, making use of Ajax techniques     | ?     | ?     | ?    |
 ^TReaDS     | 2010     | ?     | ?     | Renda et al 2010(([[http://bioalgo.iit.cnr.it/papers/TReaDS-IIT-TR06-08.pdf|Renda, E., Vecchio, A., and Pellegrini, M. (2011). TReaDS: Tandem Repeats Discovery Service. In BITS’11 (Pisa, Italy), pp. 102-104.]]))      | ?     | Includes Approximate Tandem Repeat Hunter (ATRHunter), mreps, Tandem Repeat finder (TRF), TandemSwan, TRStalker (new algorithm, only available on TReaDS)     | ?     | ?     | ?     | ?     | ?     | [[http://yucca.iit.cnr.it:8080/treads/|Yes]]     | ? Availability unknown, contact the [[mailto:[email protected];[email protected];[email protected]|authors]]     | ?     | ?     | ?     | ?     | ?    |
@@ Line 125: / Line 125: @@
 Thurston and Field 2005(([[http://www.genomics.ceh.ac.uk/msatfinder/|Thurston, M. I., and Field, D. (2006). Msatfinder, (Oxford, UK: Centre for Ecology and Hydrology. Computer program)]])) No published description of the algorithm could be found. According to the online access, regular expression (regex), multipass or iterative search engines can be used.
-==Fireusat==
+==FireµSat==
-de Riddera at al 2006(([[http://portal.acm.org/citation.cfm?doid=1216262.1216289|de Riddera, C., Kourie, D. G., and Watson, B. W. (2006). FireμSat. In Proceedings of the 2006 annual research conference of the South African institute of computer scientists and information technologists on IT research in developing couuntries  - SAICSIT  ’06 (Somerset West, South Africa), pp. 247-256.]])) Is a combination of straightforward FA technology combined with a flavour of Moore machine technology. It uses regular expressions.
+de Ridder at al 2006(([[http://portal.acm.org/citation.cfm?doid=1216262.1216289|de Riddera, C., Kourie, D. G., and Watson, B. W. (2006). FireµSat. In Proceedings of the 2006 annual research conference of the South African institute of computer scientists and information technologists on IT research in developing couuntries  - SAICSIT  ’06 (Somerset West, South Africa), pp. 247-256.]])) and de Ridder at al 2013(([[http://www.sciencedirect.com/science/article/pii/S1570866712001657|De Ridder, C., D.G. Kourie, B.W. Watson, T.R. Fourie, and P.V. Reyneke (2013). Fine-tuning the search for microsatellites. Journal of Discrete Algorithms 20: 21–37.]])), Is a combination of straightforward FA technology combined with a flavour of Moore machine technology. It uses Counting Finite Automata, which are regular language acceptors. The parameters details are the following:
+  * Max Motif Error: Is the number of motif errors the user wants to allow per motif (mutations/ motif errors allowed: deletions, mismatches, insertions).
+  * Max adjacent ATR elements: The number of ATREs that the user allows next to each other.
+  * Motif Range Options: The motif range option enables the user to specify a range of motifs FireµSat should search for.
+  * Min required TR elements: Indicates the minimum number of TREs that should occur before a TR is output – this parameter serves as a length filter.
+  * Mismatch penalty (m_p):  The penalty value allocated to a mismatch.
+  * Delete penalty (d_p):  The penalty value assigned to a deletion.
+  * Insert penalty (i_p):  The penalty value allocated to an insertion.
+  * Max substring error: Is a threshold value that the user enters. The substring error should always be smaller than the Max substring error. The calculation of the substring-error (α) is simply: α = (m_p x n_m) + (i_p x n_i) + (p_d + n_d) where Mismatch count (n_m) is the number of mismatches; delete count (n_d) is the number of deletions and insert count (n_i) is the number of insertions.
 ==Phobos==
@@ Line 152: / Line 162: @@
 Otto et al 2008(([[http://www.biomedcentral.com/1471-2105/9/366|Otto, T. D., Gomes, L. H. F., Alves-Ferreira, M., de Miranda, A. B., and Degrave, W. M. (2008). ReRep: Computational detection of repetitive sequences in genome survey sequences (GSS). BMC Bioinformatics 9, 366.]])) It is a pipeline that is based on similarity searches, the interpretation of sequence landscapes (SL), the assembly of clustered sequences and in-house Perl scripts. First, all reads are compared to each other with BLAST, with a word size of 8 and an e-value cut-off of 10-20, or with NUCMER tool, with a word size of 11. Each result is pre-processed by joining overlapping hits and by deleting self-hits. For each read, an SL is constructed by counting how often each base of the read is part of a hit with another read. Generate the graph using external tools. The minimal length that an alignment must have to enter into the analysis was defined as l. Runs with different values for l can be performed.
-==t-REKS==
+==T-REKS==
 Jorda and Kajava 2009(([[http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/btp482|Jorda, J., and Kajava, A. V. (2009). T-REKS: identification of Tandem REpeats in sequences with a K-meanS based algorithm. Bioinformatics 25, 2632-2638.]])) Mainly designed for amino acid repeats. Based on clustering of lengths between identical short strings by using a K-means algorithm and on the idea that in a tandem repeat region, the most frequently occurred length between identical SSs should be equal to the repeat length. Therefore, detection of regions of an analyzed sequence where certain lengths between identical SSs have anomalously high occurrence may lead to the localization of the tandem repeats. Steps are as follow: 1) Short string probes and K-means clustering (Use K-means algorithm for unsupervised classification) 2) Establishment of tandem repeat lengths 3) Contiguity filtering, results in identification of hypothetical repeats 4) Extension and bridging of runs 5) Similarity filtering using a build-in program based on “center-star algorithm”, CLUSTALW and MUSCLE.
@@ Line 158: / Line 168: @@
 Pokrzywa and Polanski 2010(([[http://linkinghub.elsevier.com/retrieve/pii/S0888754310001758|Pokrzywa, R., and Polanski, A. (2010). BWtrs: A tool for searching for tandem repeats in DNA sequences based on the Burrows–Wheeler transform. Genomics 96, 316-321.]])) It is an efficient data compression algorithm based on the idea of backward search with the Burrows–Wheeler Transform (BWT) algorithm. It allows listing all occurrences of exact tandem repeats in a given string of length n in O(n log n) time. It then uses the efficient string indexing structure by Ferragina and Manzini for searching for the occurrences of so called rearmost tandem repeats that are then used to list the locations of the desire preferred tandem repeats, namely, the maximal tandem repeats of the primitive motif.
-==QDD==
+==QDD, QDD2==
-Meglecz et al 2010(([[http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/btp670|Meglecz, E., Costedoat, C., Dubut, V., Gilles, A., Malausa, T., Pech, N., and Martin, J.-F. (2009). QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects. Bioinformatics 26, 403-404.]])) The algorithm takes the following steps: 1) Sequence cleaning and microsatellite detection (Sort according to sequence tags, trims vector and adaptors sequences). 2) Sequence similarity detection (Is time consuming, is meant to remove redundancy, and sequences that are part of a repetitive region of the genome). 3) Microsatellite selection and primer design (Selection of sequences that contain a target microsatellite and a flanking region free from very short repetitions; and primer selection using Primer3).
+Meglecz et al 2010(([[http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/btp670|Meglecz, E., Costedoat, C., Dubut, V., Gilles, A., Malausa, T., Pech, N., and Martin, J.-F. (2009). QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects. Bioinformatics 26, 403-404.]])) The algorithm takes the following steps:
+  - Sequence cleaning and microsatellite detection (Sort according to sequence tags, trims vector and adaptors sequences).
+  - Sequence similarity detection (Is time consuming, is meant to remove redundancy, and sequences that are part of a repetitive region of the genome).
+  - Iterative primer design using Primer3. Iterations (a) from designing primers only for perfect microsatellites with no short repeats in the flanking region till allowing multiple target microsatellites, short repetitions and homopolymers in the amplified region (b) produce primer pairs with PCR products in different size ranges.
+  - BLASTs selected sequences to Genbank to detect serious contaminations or mixing up samples.