SplicedFamAlign: CDS-to-gene spliced alignment and identification of transcript orthology groups.

ABSTRACT:

Background

The inference of splicing orthology relationships between gene transcripts is a basic step for the prediction of transcripts and the annotation of gene structures in genomes. The splicing structure of a sequence refers to the exon extremity information in a CDS or the exon-intron extremity information in a gene sequence. Splicing orthologous CDS are pairs of CDS with similar sequences and conserved splicing structures from orthologous genes. Spliced alignment that consists in aligning a spliced cDNA sequence against an unspliced genomic sequence, constitutes a promising, yet unexplored approach for the identification of splicing orthology relationships. Existing spliced alignment algorithms do not exploit the information on the splicing structure of the input sequences,

SUBMITTER: Jammali S 

PROVIDER: S-EPMC6439985 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature