AceView: a comprehensive cDNA-supported gene and transcripts annotation.

ABSTRACT:

Background

Regions covering one percent of the genome, selected by ENCODE for extensive analysis, were annotated by the HAVANA/Gencode group with high quality transcripts, thus defining a benchmark. The ENCODE Genome Annotation Assessment Project (EGASP) competition aimed at reproducing Gencode and finding new genes. The organizers evaluated the protein predictions in depth. We present a complementary analysis of the mRNAs, including alternative transcript variants.

Results

We evaluate 25 gene tracks from the University of California Santa Cruz (UCSC) genome browser. We either distinguish or collapse the alternative splice variants, and compare the genomic coordinates of exons, introns and nucleotides. Whole mRNA models, seen as chains of introns, are sorted to find the best

SUBMITTER: Thierry-Mieg D 

PROVIDER: S-EPMC1810549 | biostudies-literature | 2006

REPOSITORIES: biostudies-literature