PLAST-ncRNA: Partition function local alignment search tool for non-coding RNA sequences

Satish Chikkagoudar, Dennis R. Livesay, Usman Roshan

Research output: Contribution to journalArticlepeer-review

7 Scopus citations

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.

Original languageEnglish (US)
Article numbergkq487
Pages (from-to)W59-W63
JournalNucleic Acids Research
Volume38
Issue numberSUPPL. 2
DOIs
StatePublished - Jun 3 2010

All Science Journal Classification (ASJC) codes

  • Genetics

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