Pfam in UCSC Gene Track Settings
 
Pfam Domains in UCSC Genes   (All Genes and Gene Predictions tracks)

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Data last updated: 2013-07-01

Description

Most proteins are composed of one or more conserved functional regions called domains. This track shows the high-quality, manually-curated Pfam-A domains found in transcripts located in the UCSC Genes track.

Display Conventions and Configuration

This track follows the display conventions for gene tracks.

Methods

The sequences from the knownGenePep table (see UCSC Genes description page) are submitted to the set of Pfam-A HMMs which annotate regions within the predicted peptide that are recognizable as Pfam protein domains. These regions are then mapped to the transcripts themselves using the pslMap utility.

Credits

pslMap was written by Mark Diekhans at UCSC.

References

Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K et al. The Pfam protein families database. Nucleic Acids Res. 2010 Jan;38(Database issue):D211-22.