title: PHAT: a transmembrane-specific substitution matrix. Predicted hydrophobic and transmembrane.
abstract: BACKGROUND
  Database searching algorithms for proteins use scoring matrices based on average protein properties, and thus are dominated by globular proteins. However, since transmembrane regions of a protein are in a distinctly different environment than globular proteins, one would expect generalized substitution matrices to be inappropriate for transmembrane regions.
  
  
  RESULTS
  We present the PHAT (predicted hydrophobic and transmembrane) matrix, which significantly outperforms generalized matrices and a previously published transmembrane matrix in searches with transmembrane queries. We conclude that a better matrix can be constructed by using background frequencies characteristic of the twilight zone, where low-scoring true positives have scores indistinguishable from high-scoring false positives, rather than the amino acid frequencies of the database. The PHAT matrix may help improve the accuracy of sequence alignments and evolutionary trees of membrane proteins.
authors: Department of Bioengineering, University of Washington, Seattle, WA 98195, USA.
authors: P C
authors: PC
authors: Ng
authors: J G
authors: JG
authors: Henikoff
authors: S
authors: S
authors: Henikoff
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D016384:Consensus Sequence / Q000235:genetics; D016208:Databases, Factual; D008565:Membrane Proteins / Q000235:genetics*; D008962:Models, Theoretical; D011237:Predictive Value of Tests; D011506:Proteins / Q000737:chemistry / Q000235:genetics; D015203:Reproducibility of Results; D016415:Sequence Alignment / Q000379:methods*; D017386:Sequence Homology, Amino Acid
chemical_list: D008565:Membrane Proteins; D011506:Proteins