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Database (Oxford). 2012 Mar 20;2012:bas003. doi: 10.1093/database/bas003. Print 2012.

AntiFam: a tool to help identify spurious ORFs in protein annotation.

Author information

  • 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA. UK. re3@sanger.ac.uk

Abstract

As the deluge of genomic DNA sequence grows the fraction of protein sequences that have been manually curated falls. In turn, as the number of laboratories with the ability to sequence genomes in a high-throughput manner grows, the informatics capability of those labs to accurately identify and annotate all genes within a genome may often be lacking. These issues have led to fears about transitive annotation errors making sequence databases less reliable. During the lifetime of the Pfam protein families database a number of protein families have been built, which were later identified as composed solely of spurious open reading frames (ORFs) either on the opposite strand or in a different, overlapping reading frame with respect to the true protein-coding or non-coding RNA gene. These families were deleted and are no longer available in Pfam. However, we realized that these may perform a useful function to identify new spurious ORFs. We have collected these families together in AntiFam along with additional custom-made families of spurious ORFs. This resource currently contains 23 families that identified 1310 spurious proteins in UniProtKB and a further 4119 spurious proteins in a collection of metagenomic sequences. UniProt has adopted AntiFam as a part of the UniProtKB quality control process and will investigate these spurious proteins for exclusion.

PMID:
22434837
[PubMed - indexed for MEDLINE]
PMCID:
PMC3308159
Free PMC Article

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