YASS (Yet Another Similarity Searcher) is a free software, pairwise sequence alignment software for nucleotide sequences, that is, it can search for similarities between DNA or RNA sequences. YASS accepts nucleotide sequences in either plain text or the FASTA format and the output format includes the BLAST tabular output. YASS uses several transition-constrained spaced seed k-mers, which allow considerably improved sensitivity. YASS can be used locally on a user's machine, or as SaaS on the YASS web server, which produces a browser based dot-plot.
See also
External links
References
Noe L., Kucherov. G. (2005). "YASS: enhancing the sensitivity of DNA similarity search". Nucleic Acids Research. 33 (2): W540 – W543. doi:10.1093/nar/gki478. PMC 1160238. PMID 15980530. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160238 ↩
Noe L., Kucherov. G. (2004). "Improved hit criteria for DNA local alignment". BMC Bioinformatics. 5: 149. doi:10.1186/1471-2105-5-149. PMC 526756. PMID 15485572. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC526756 ↩
"README". Retrieved 7 April 2015. https://bioinfo.univ-lille.fr/yass/files/yass-current/README ↩