A method of precise mRNA/DNA homology-based gene structure prediction.

ABSTRACT:

Background

Accurate and automatic gene finding and structural prediction is a common problem in bioinformatics, and applications need to be capable of handling non-canonical splice sites, micro-exons and partial gene structure predictions that span across several genomic clones.

Results

We present a mRNA/DNA homology based gene structure prediction tool, GIGOgene. We use a new affine gap penalty splice-enhanced global alignment algorithm running in linear memory for a high quality annotation of splice sites. Our tool includes a novel algorithm to assemble partial gene structure predictions using interval graphs. GIGOgene exhibited a sensitivity of 99.08% and a specificity of 99.98% on the Genie learning set, and demonstrated a higher quality of gene structural prediction whe

SUBMITTER: Churbanov A 

PROVIDER: S-EPMC1274302 | biostudies-literature | 2005 Oct

REPOSITORIES: biostudies-literature