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


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.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 data are available at Bioinformatics online.

SUBMITTER: Kim BH 

PROVIDER: S-EPMC2881392 | biostudies-literature | 2010 Jun

REPOSITORIES: biostudies-literature

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

Kim Bong-Hyun BH   Cong Qian Q   Grishin Nick V NV  

Bioinformatics (Oxford, England) 20100422 12


<h4>Unlabelled</h4>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-BLA  ...[more]

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