PLAST-ncRNA: Partition function Local Alignment Search Tool for non-coding RNA sequences.
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.
Chikkagoudar
Satish
S
Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA.
Livesay
Dennis R
DR
Roshan
Usman
U
D000465:Algorithms; D020407:Internet; D022661:RNA, Untranslated / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D014584:User-Computer Interface
D022661:RNA, Untranslated