Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner.

ABSTRACT:

Motivation

The most accurate way to determine the intron-exon structures in a genome is to align spliced cDNA sequences to the genome. Thus, cDNA-to-genome alignment programs are a key component of most annotation pipelines. The scoring system used to choose the best alignment is a primary determinant of alignment accuracy, while heuristics that prevent consideration of certain alignments are a primary determinant of runtime and memory usage. Both accuracy and speed are important considerations in choosing an alignment algorithm, but scoring systems have received much less attention than heuristics.

Results

We present Pairagon, a pair hidden Markov model based cDNA-to-genome alignment program, as the most accurate aligner for sequences with high- and low-identity levels. We

SUBMITTER: Lu DV 

PROVIDER: S-EPMC2732315 | biostudies-literature | 2009 Jul

REPOSITORIES: biostudies-literature