Searching for evolutionary distant RNA homologs within genomic sequences using partition function posterior probabilities

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 structuresequence 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. Results: We create a pairwise RNA-genome alignment benchmark from RFAM families with average pairwise sequence identity up to 60%. Each dataset contains a query RNA aligned to a target RNA (of the same family) embedded in a genomic sequence at least 5K nucleotides long. To simulate common cond...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Usman Roshan, Satish Chikkagoudar, Dennis R. Livesay
• Keywords: Alignment Programs, BMCBI 2008, Local Alignment, Pairwise Sequence Identity