Wolfram Höps, BCCN Berlin/TU Berlin

Gene Unprediction: Developing a new method to identify spurious protein sequences

We now have access to the sequences of tens of millions of proteins. The vast majority of protein sequences are derived from gene prediction tools and have no experimental supporting evidence for their translation. Despite the increasing accuracy of gene prediction tools there likely exists a large number of spurious protein predictions in the sequence databases. We have developed the Spurio tool to help identify spurious protein predictions in prokaryotes. Spurio searches the query protein sequence against a prokaryotic nucleotide database using tblastn and identifies homologous sequences. The tblastn matches are used to score the query sequence’s likelihood of being a spurious protein prediction using a Gaussian process model. The most informative feature is the appearance of stop codons within the presumed translation of homologous DNA sequences. Benchmarking shows that the Spurio tool is able to distinguish spurious from true proteins in most cases. Our initial experiments suggest that less than 1% of the proteins in the UniProtKB sequence database are likely to be spurious and that Spurio is able to identify over 60 times more spurious proteins than the previously developed AntiFam resource.

Additional Information

Master thesis defense in the International Master Program Computational Neuroscience.

Organized by

Hans-Peter Herzel / Robert Martin

Location

BCCN Berlin, lecture hall, Philippstr. 13 Haus 6, 10115 Berlin