TABLE 5.
Tools for detecting SSR part 2 – basic tools for perfect and Imperfect SSR analysis.
| Name | Reference/Year | 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IMEx | Mudunuri 2007 | IMEx | No | Linux, Web | Graphical Interface and Command Line | SSR | 1–6 bp | FASTA; PTT | No | Yes | Yes | Yes | No | http://www.mcr.org.in/IMEX/download.html |
| Imperfect SSR Finder | Stieneke 2007 | Imperfect SSR Finder | No | Web | Graphical interface | SSR | 2–10 bp | FASTA | No | Yes | Yes | Yes | No | https://ssr.nwisrl.ars.usda.gov/ |
| Microsatellite repeats finder | Bikandi 2006 | Microsatellite repeats finder | No | Web | Graphical Interface | SSR | 2–10 bp | DNA Sequence | No | Yes | Yes | No | No | http://insilico.ehu.es/mini_tools/microsatellites/?info |
| Sputnik | Morgante 2002 | Sputnik | No | Linux, Windows | Command Line | SSR | 1–5 bp | FASTA | No | Yes | Yes | No | No | http://wheat.pw.usda.gov/ITMI/EST-SSR/LaRota/ |
“Yes” has been highlighted in the columns for visualization purposes. “SSR” = Simple Sequence Repeats or microsatellite. “BP” = Base pair. “p-SSR” = Perfect SSR. “i-SSR” = Imperfect SSR. “c-SSR” = Compound SSR.