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

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

Author information

1
Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA. kim@chop.swmed.edu

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.

PMID:
20413635
PMCID:
PMC2881392
DOI:
10.1093/bioinformatics/btq208
[Indexed for MEDLINE]
Free PMC Article

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