title: 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.
  
  
  BACKGROUND
  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/.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA. kim@chop.swmed.edu
authors.forename: Bong-Hyun
authors.initials: BH
authors.lastname: Kim
authors.forename: Qian
authors.initials: Q
authors.lastname: Cong
authors.forename: Nick V
authors.initials: NV
authors.lastname: Grishin
mesh_terms: D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins