ProTISA: a comprehensive resource for translation initiation site annotation in prokaryotic genomes

Nucleic Acids Res. 2008 Jan;36(Database issue):D114-9. doi: 10.1093/nar/gkm799. Epub 2007 Oct 16.

Abstract

Correct annotation of translation initiation site (TIS) is essential for both experiments and bioinformatics studies of prokaryotic translation initiation mechanism as well as understanding of gene regulation and gene structure. Here we describe a comprehensive database ProTISA, which collects TIS confirmed through a variety of available evidences for prokaryotic genomes, including Swiss-Prot experiments record, literature, conserved domain hits and sequence alignment between orthologous genes. Moreover, by combining the predictions from our recently developed TIS post-processor, ProTISA provides a refined annotation for the public database RefSeq. Furthermore, the database annotates the potential regulatory signals associated with translation initiation at the TIS upstream region. As of July 2007, ProTISA includes 440 microbial genomes with more than 390 000 confirmed TISs. The database is available at http://mech.ctb.pku.edu.cn/protisa.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Codon, Initiator*
  • Databases, Nucleic Acid* / statistics & numerical data
  • Genome, Archaeal*
  • Genome, Bacterial*
  • Genomics
  • Internet
  • Peptide Chain Initiation, Translational*
  • Regulatory Sequences, Nucleic Acid*
  • User-Computer Interface

Substances

  • Codon, Initiator