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HangOut: generating clean PSI-BLAST profiles for domains with long insertions
Bong-Hyun Kim1, Qian Cong, Nick V Grishin
1Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA. kim@chop.swmed.edu
Bioinformatics (Oxford, England)
|April 24, 2010
Summary
Profile corruption in protein similarity searches can lead to errors. The HangOut procedure cleans alignments to generate more accurate protein profiles, improving structure-function studies.
Area of Science:
- Computational biology
- Bioinformatics
- Protein structure analysis
Background:
- Profile-based similarity search is crucial for protein structure-function studies.
- Profile corruption, often from non-homologous segments in multidomain proteins, leads to false positives.
- Single domains with long insertions are a significant source of alignment errors.
Purpose of the Study:
- To develop a method for cleaning erroneously extended PSI-BLAST alignments.
- To improve the accuracy of protein profiles generated from sequence data.
- To reduce false positives in profile-based similarity searches.
Main Methods:
- Developed a procedure named HangOut.
- HangOut specifically targets single domains with specified insertion positions.
- The method cleans PSI-BLAST alignments to correct profile corruption.
Main Results:
- HangOut generates cleaner profiles by removing erroneous extensions in alignments.
- This leads to more reliable profile-based similarity search results.
- The procedure effectively addresses errors common in multidomain proteins.
Conclusions:
- The HangOut procedure offers a robust solution for profile corruption in protein sequence analysis.
- Improved protein profiles enhance the accuracy of structure-function relationship studies.
- This method contributes to more reliable identification of homologous protein domains.
