HangOut: Generating clean PSI-BLAST profiles for domains with long insertions

Bong Hyun Kim, Qian Cong, Nick V. Grishin

Research output: Contribution to journalArticle

5 Scopus citations

Abstract

Summary: 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/. Contact: kim@chop.swmed.edu; grishin@chop.swmed.edu. Supplementary information: Supplementary data are available at Bioinformatics online.

Original languageEnglish (US)
Article numberbtq208
Pages (from-to)1564-1565
Number of pages2
JournalBioinformatics
Volume26
Issue number12
DOIs
StatePublished - Apr 22 2010

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ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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