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

Satish Chikkagoudar; Dennis R. Livesay; Usman Roshan

doi:10.1093/nar/gkq487

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

Satish Chikkagoudar, Dennis R. Livesay, Usman Roshan

Research output: Contribution to journal › Article › peer-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 language	English (US)
Article number	gkq487
Pages (from-to)	W59-W63
Journal	Nucleic Acids Research
Volume	38
Issue number	SUPPL. 2
DOIs	https://doi.org/10.1093/nar/gkq487
State	Published - Jun 3 2010

All Science Journal Classification (ASJC) codes

Genetics

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10.1093/nar/gkq487

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title = "PLAST-ncRNA: Partition function local alignment search tool for non-coding RNA sequences",

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.",

author = "Satish Chikkagoudar and Livesay, {Dennis R.} and Usman Roshan",

note = "Funding Information: United States National Science Foundation (grant 033-1654 to CIPRES cluster). Funding for open access charge: United States National Science Foundation.",

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AU - Chikkagoudar, Satish

AU - Livesay, Dennis R.

AU - Roshan, Usman

N1 - Funding Information: United States National Science Foundation (grant 033-1654 to CIPRES cluster). Funding for open access charge: United States National Science Foundation.

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N2 - 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.

AB - 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.

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

Abstract

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