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 GENCODE Genes track by the software HMMER3.

Display Conventions and Configuration

This track follows the display conventions for gene tracks.

Methods

The sequences from the knownGenePep table (see GENCODE 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. A complete shell script log for every version of UCSC genes can be found in our GitHub repository under hg/makeDb/doc/ucscGenes, e.g. mm10.knownGenes17.csh is for the database mm10 and version 17 of UCSC known genes.

Of the several options for filtering out false positives, the "Trusted cutoff (TC)" threshold method is used in this track to determine significance. For more information regarding thresholds and scores, see the HMMER documentation and results interpretation pages.

Note: There is currently an undocumented but known HMMER problem that results in lessened sensitivity and possible missed searches for some zinc finger domains. Until a fix is released for HMMER /PFAM thresholds, please also consult the "UniProt Domains" subtrack of the UniProt track for more comprehensive zinc finger annotations.

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. PMID: 19920124; PMC: PMC2808889