HangOut: Generating Clean PSI-BLAST Profiles for Domains With Long Insertions

Bioinformatics. 2010 Jun 15;26(12):1564-5. doi: 10.1093/bioinformatics/btq208. Epub 2010 Apr 22.

Abstract

Profile-based similarity search is an essential step in structure-function studies of proteins. However, inclusion of non-homologous sequence segments into a profile causes its corruption and results in false positives. Profile corruption is common in multidomain proteins, and single domains with long insertions are a significant source of errors. We developed a procedure (HangOut) that, for a single domain with specified insertion position, cleans erroneously extended PSI-BLAST alignments to generate better profiles.

Availability: HangOut is implemented in Python 2.3 and runs on all Unix-compatible platforms. The source code is available under the GNU GPL license at http://prodata.swmed.edu/HangOut/.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Protein Structure, Tertiary*
  • Proteins / chemistry
  • Sequence Alignment / methods*
  • Sequence Analysis, Protein / methods*
  • Software*

Substances

  • Proteins