Searching for evolutionary distant RNA homologs within genomic sequences using partition function posterior probabilities |
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Authors: | Usman Roshan Satish Chikkagoudar Dennis R Livesay |
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Affiliation: | (1) Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, USA;(2) Department of Computer Science and Bioinformatics Research Center, University of North Caroline at Charlotte, Charlotte, NC, USA |
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Abstract: | Background Identification of RNA homologs within genomic stretches is difficult when pairwise sequence identity is low or unalignable flanking residues are present. In both cases structure-sequence or profile/family-sequence alignment programs become difficult to apply because of unreliable RNA structures or family alignments. As such, local sequence-sequence alignment programs are frequently used instead. We have recently demonstrated that maximal expected accuracy alignments using partition function match probabilities (implemented in Probalign) are significantly better than contemporary methods on heterogeneous length protein sequence datasets, thus suggesting an affinity for local alignment. |
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