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