PLAST-ncRNA: Partition function Local Alignment Search Tool for non-coding RNA sequences
Autor: | Satish Chikkagoudar, Dennis R. Livesay, Usman Roshan |
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Jazyk: | angličtina |
Rok vydání: | 2010 |
Předmět: |
Smith–Waterman algorithm
Internet Multiple sequence alignment RNA Untranslated Sequence analysis business.industry Sequence Analysis RNA Structural alignment Posterior probability Sequence alignment Pattern recognition Articles Biology Bioinformatics User-Computer Interface ComputingMethodologies_PATTERNRECOGNITION Sequence Homology Nucleic Acid Genetics Consensus sequence Artificial intelligence business Sequence Alignment Alignment-free sequence analysis Algorithms Software |
Zdroj: | Nucleic Acids Research |
ISSN: | 1362-4962 0305-1048 |
Popis: | 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. |
Databáze: | OpenAIRE |
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