PHAT matrices : Matrices for transmembrane proteins

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The PHAT matrices
A Matrix Series for Transmembrane Regions

Submit a transmembrane protein sequence (aligns transmembrane sequences with the PHAT matrix)
Sequence converted to profile format for SWAT (for those who want to run their searches locally)
The PHAT matrix series are built from predicted hydrophobic and transmembrane regions. It performs significantly better at database searching on transmembrane regions than any previously published matrix.

Database searching algorithms for proteins use a scoring matrix that is based on average protein properties and is dominated by globular proteins. However, transmembrane regions of a protein are in a distinctly different environment than globular proteins. Hence, one would expect the substitution scores to differ and a matrix specialized for transmembrane regions to work better than matrices that have been generalized for all proteins.

A substitution score for amino acid i to j can be calculated from alignment data by:

sij = C log (pij / qiqj)
where C is a constant, pij's are the target or observed frequencies and qi's are the background frequencies (see Altschul, 1991 for details).
The PHAT matrix series are built from target frequencies obtained from BLOCKS predicted to be transmembrane by PHDhtm and background frequencies from hydrophobic and transmembrane regions as determined by Persson-Argos transmembrane propensity values:
sijPHAT = C log (pijPHDhtm / qiP-Aq jP-A)
The PHAT matrix series have been shown to work significantly better than BLOSUM62 (Henikoff and Henikoff, 1992) , JTT-modified PAM (Jones, Taylor, Thornton, 1992) , and other transmembrane matrices (Jones, Taylor, Thornton, 1994) .
For more details, see our paper:
PHAT: a transmembrane-specific substitution matrix
(Ng, Henikoff, Henikoff 2000 Bioinformatics 16: 760-766 + Errata in Bioinformatics 17:290)
If you do not have access to Bioinformatics, you can also download the manuscript here (that have the correct figures).

You can download the matrices here.
PHAT matrices series
Persson-Argos matrix series
PHDhtm matrix series
Submit a transmembrane protein sequence

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