Seq2Ref: A web server to facilitate functional interpretation

Wenlin Li, Qian Cong, Lisa N. Kinch, Nick V. Grishin

Research output: Contribution to journalArticlepeer-review

5 Scopus citations


Background: The size of the protein sequence database has been exponentially increasing due to advances in genome sequencing. However, experimentally characterized proteins only constitute a small portion of the database, such that the majority of sequences have been annotated by computational approaches. Current automatic annotation pipelines inevitably introduce errors, making the annotations unreliable. Instead of such error-prone automatic annotations, functional interpretation should rely on annotations of 'reference proteins' that have been experimentally characterized or manually curated.Results: The Seq2Ref server uses BLAST to detect proteins homologous to a query sequence and identifies the reference proteins among them. Seq2Ref then reports publications with experimental characterizations of the identified reference proteins that might be relevant to the query. Furthermore, a plurality-based rating system is developed to evaluate the homologous relationships and rank the reference proteins by their relevance to the query.Conclusions: The reference proteins detected by our server will lend insight into proteins of unknown function and provide extensive information to develop in-depth understanding of uncharacterized proteins. Seq2Ref is available at:

Original languageEnglish (US)
Article number30
JournalBMC Bioinformatics
Issue number1
StatePublished - Jan 28 2013


  • Functional interpretation
  • PubMed literature
  • Reference protein
  • Sequence homology
  • Web server

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics


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