Difference between revisions of "YASS"
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|sw summary=YASS is a genomic similarity search tool, for nucleic (DNA/RNA) sequences in fasta or plain text format (it produces local pairwise alignments). | |sw summary=YASS is a genomic similarity search tool, for nucleic (DNA/RNA) sequences in fasta or plain text format (it produces local pairwise alignments). | ||
|created by=Kucherov G, Noe L | |created by=Kucherov G, Noe L | ||
| − | |created at= LIFL Bioinfo / INRIA Lille-Nord Europe Sequoia group | + | |created at=LIFL Bioinfo / INRIA Lille-Nord Europe Sequoia group |
| + | |email address=laurent.noe@univ-lille1.fr | ||
}} | }} | ||
| + | == Description == | ||
| + | <!-- Describe the application in the space below --> | ||
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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). | 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). | ||
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{{Links}} | {{Links}} | ||
{{References}} | {{References}} | ||
{{Link box}} | {{Link box}} | ||
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Latest revision as of 19:46, 3 December 2015
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Application data |
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| Created by | Kucherov G, Noe L |
|---|---|
| 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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