HangOut: generating clean PSI-BLAST profiles for domains with long insertions.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 20413635.
- Also identified by DOI 10.1093/bioinformatics/btq208 and PMC identifier 2881392.
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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.
Medical subject headings
- Protein Structure, Tertiary
- Sequence Alignment
- Sequence Analysis, Protein
- Software