Abstract:
:Alignment-based programs are valuable tools for finding potential homologs in genome sequences. Previously, it has been shown that partition function posterior probabilities attuned to local alignment achieve a high accuracy in identifying distantly similar non-coding RNA sequences that are hidden in a large genome. Here, we present an online implementation of that alignment algorithm based on such probabilities. Our server takes as input a query RNA sequence and a large genome sequence, and outputs a list of hits that are above a mean posterior probability threshold. The output is presented in a format suited to local alignment. It can also be viewed within the PLAST alignment viewer applet that provides a list of all hits found and highlights regions of high posterior probability within each local alignment. The server is freely available at http://plastrna.njit.edu.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Chikkagoudar S,Livesay DR,Roshan Udoi
10.1093/nar/gkq487subject
Has Abstractpub_date
2010-07-01 00:00:00pages
W59-63issue
Web Server issueeissn
0305-1048issn
1362-4962pii
gkq487journal_volume
38pub_type
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