TABLE 3.
Tools for detecting repetitive elements (RE) and tandem repeats (TR).
| Name | Reference/Year | Type | Mining tool | Integrated toolset | Platform | Execution | Focus | Max motif lenght | Input files | Output graphs/Charts | p-SSR | i-SSR | c-SSR | Primer design | Tool’s link |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| RepeatMasker | Smit 1996 apud Tarailo-Graovac 2009 | Pipeline Tool | RepeatMasker | cross_match, WU-BLAST | Linux, Web | Graphical Interface and Command Line | RE | No limit | FASTA | No | Yes | Yes | No | No | https://www.repeatmasker.org/cgi-bin/WEBRepeatMasker |
| REPuter | Kurtz 2001 | Basic tool | REPuter | No | Linux, Mac OS, Web | Graphical Interface and Command Line | RE | <5 000 bp | DNA sequence | Yes | Yes | Yes | Yes | No | http://bibiserv.techfak.uni-bielefeld.de/reputer/ |
| Spectral-repeat finder | Sharma 2004 | Basic tool | Spectral-repeat finder | No | Linux, Mac OS, Windows, Web | Graphical Interface | RE | No limit | FASTA; GBK | No | Yes | Yes | No | No | http://www.imtech.res.in/raghava/srf |
| Dot2Dot | Genovese 2019 | Basic tool | Dot2Dot | No | Linux, Mac OS | Command Line | TR | No limit | FASTA; FASTQ | No | Yes | Yes | No | No | https://github.com/Gege7177/Dot2dot |
| Etandem/Equicktandem | Rice 2000 | Basic tool | Etandem/Equicktandem | No | Linux | Command Line | TR | 1–600 bp | FASTA; GBK; GFF; EMBL and Others | No | Yes | No | No | No | https://www.bioinformatics.nl/cgi-bin/emboss/help/equicktandem |
| Mreps | Kolpakov 2003 | Basic tool | Mreps | No | Linux, Windows, Web | Graphical Interface and Command Line | TR | No limit | FASTA | No | Yes | Yes | No | No | https://mreps.univ-mlv.fr/ |
| STAR | Delgrange 2004 | Basic tool | STAR | No | Linux, Mac OS, Windows, Web | Graphical Interface and Command Line | TR | No limit | FASTA | No | Yes | Yes | No | No | http://atgc.lirmm.fr/star/ |
| T-reks | Jorda 2009 | Pipeline Tool | T-reks | CLUSTALW, MUSCLE | Linux, Mac OS, Windows, Web | Graphical Interface and Command Line | TR | No limit | FASTA | No | Yes | Yes | No | No | https://bioinfo.crbm.cnrs.fr/index.php?route=tools&tool=3 |
| TRF | Benson 1999 | Basic tool | TRF | No | Linux, Mac OS, Windows, Web | Graphical Interface and Command Line | TR | 1–5, 10–2000 bp | FASTA | No | Yes | Yes | No | No | https://tandem.bu.edu/trf/trf.html |
“Yes” and “Pipeline” have been highlighted in the columns for visualization purposes. “RE” = repetitive elements, “TR” = Tandem Repeats. “BP” = Base pair. “p-SSR” = Perfect SSR. “i-SSR” = Imperfect SSR. “c-SSR” = Compound SSR.