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

Document Type

Article

Publication Date

6-3-2010

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. © The Author(s) 2010. Published by Oxford University Press.

Identifier

77954299062 (Scopus)

Publication Title

Nucleic Acids Research

External Full Text Location

https://doi.org/10.1093/nar/gkq487

e-ISSN

13624962

ISSN

03051048

PubMed ID

20522510

First Page

W59

Last Page

W63

Issue

SUPPL. 2

Volume

38

Grant

033-1654

Fund Ref

National Science Foundation

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