YASS
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Application data |
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| Created by | Kucherov G, Noe L |
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| Created at | LIFL Bioinfo / INRIA Lille-Nord Europe Sequoia group |
| Maintained? | Maybe |
| Contact: | laurent.noe@univ-lille1.fr |
Summary: YASS is a genomic similarity search tool, for nucleic (DNA/RNA) sequences in fasta or plain text format (it produces local pairwise alignments).
"Error: no local variable "counter" was set." is not a number.
Description
Like most of the heuristic DNA local alignment software (BLAST, FASTA, PATTERNHUNTER, BLASTZ ...), YASS uses seeds to detect potential similarity regions, and then tries to extend them to actual alignments. This genomic search tool uses multiple transition constrained spaced seeds that enable to search more fuzzy repeats, as non-coding DNA/RNA. Another simple, but interesting feature is that you can specify the seed pattern used in the search step (as provided by hedera or iedera).
Links
References
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