Selenoprofiles: profile-based scanning of eukaryotic genome sequences for selenoprotein genes.

ABSTRACT:

Motivation

Selenoproteins are a group of proteins that contain selenocysteine (Sec), a rare amino acid inserted co-translationally into the protein chain. The Sec codon is UGA, which is normally a stop codon. In selenoproteins, UGA is recoded to Sec in presence of specific features on selenoprotein gene transcripts. Due to the dual role of the UGA codon, selenoprotein prediction and annotation are difficult tasks, and even known selenoproteins are often misannotated in genome databases.

Results

We present an homology-based in silico method to scan genomes for members of the known eukaryotic selenoprotein families: selenoprofiles. The core of the method is a set of manually curated highly reliable multiple sequence alignments of selenoprotein families, which are used as queri

SUBMITTER: Mariotti M 

PROVIDER: S-EPMC2958745 | biostudies-literature | 2010 Nov

REPOSITORIES: biostudies-literature