• HangOut: generating clean PSI-...

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

Title:
HangOut: generating clean PSI-BLAST profiles for domains with long insertions.
Authors:
Kim BH; Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA. kim@chop.swmed.edu, Cong Q, Grishin NV
Source:
Bioinformatics (Oxford, England) [Bioinformatics] 2010 Jun 15; Vol. 26 (12), pp. 1564-5. Date of Electronic Publication: 2010 Apr 22.
Publication Type:
Journal Article; Research Support, Non-U.S. Gov't
Language:
English
Journal Info:
Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE
Imprint Name(s):
Original Publication: Oxford : Oxford University Press, c1998-
MeSH Terms:
Protein Structure, Tertiary* , Software*, Sequence Alignment/*methods , Sequence Analysis, Protein/*methods, Proteins/chemistry
References:
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Grant Information:
United States Howard Hughes Medical Institute
Substance Nomenclature:
0 (Proteins)
Entry Date(s):
Date Created: 20100424 Date Completed: 20101021 Latest Revision: 20211020
Update Code:
20250114
PubMed Central ID:
PMC2881392
DOI:
10.1093/bioinformatics/btq208
PMID:
20413635
Database:
MEDLINE

Weitere Informationen

Unlabelled: 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.