Is there any command line or GUI software to find SSR microsatellites using pattern?
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2.3 years ago
rimgubaev ▴ 270

Hello everyone! The problem is the following: I got a pattern of microsatellite, for example (GA)8nGTGT(G)11, and I want to search for all possible targets across the specified locus (2nd chromosome) across all genome assemblies. I tried non-specific software namely BLASTn, however there is no option to choose a specific chromosome as well as to specify all assemblies available. I also tried UGENE but it also searches across one assembly. Could you suggest some tool if there is any, please?

SSR microsatellites Hordeum vulgare • 444 views
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2.3 years ago

http://emboss.sourceforge.net/apps/cvs/emboss/apps/fuzznuc.html

fuzznuc searches for a specified PROSITE-style pattern in nucleotide sequences. Such patterns are specifications of a (typically short) length of sequence to be found. They can specify a search for an exact sequence or they can allow various ambiguities, matches to variable lengths of sequence and repeated subsections of the sequence. One or more nucleotide sequences are read from file. The output is a standard EMBOSS report file that includes data such as location and score of any matches.

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A GUI for fuzznuc. Not sure if it will take chromosome sized data via web.