Instructions on Using PHAT with SWAT

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Instructions on Using PHAT with SWAT

- Why we use SWAT
- Submitting sequences
- Submitting a database

Why we use SWAT
We use SWAT (Green, P. University of Washington), a Smith-Waterman alignment tool, to align sequences because it is the only program that we know of that can accept profiles. As with any searching/alignment tool, only those with low enough E-values should be considered. Due to the time it takes to execute SWAT, our server is unable to support entire database searches and we ask that you submit your own database of sequences to search your query against.
Submitting Sequences
If your FASTA sequence looks like:

    >sp|P45090|ARTQ_HAEIN ARGININE TRANSPORT SYSTEM PERMEASE PROTEIN ARTQ - Haemophilus influenzae.
    MFSDFLSLMFTAALMTLGLAVCSLLLGLFLSLIFAVLEANRFVGKPMTVF
    VALLRGLPEIIVVLLVYFGSTELVEMLTGEYIEFGAFGCGVLALSLIFAA
    YASQTLRGAIQAIPKGQWESGAALGLSKSYTFIHIVMPQVWRHALPGLST
    QWLVLLKDTALVSLIGVDDLMHQADLINTNTHQPFTWYGIAALIYLAVTL
    ISQVGIRKLELRFTRFERGVK

Then to give transmembrane regions to the above FASTA sequence, enter a fasta-like sequence with X's for nontransmembrane amino acids and T's for amino acids considered to lie transmembrane regions.
Below is the correct format for 5 transmembrane regions in ARTQ_HAEIN that occur at positions 13-37, 47-71 , 84-103, 1 43, 167, 185-206. (These were the regions predicted by HMMTOP.)

    >sp|P45090|ARTQ_HAEIN ARGININE TRANSPORT SYSTEM PERMEASE PROTEIN ARTQ - Haemophilus influenzae.
    XXXXXXXXXXXXTTTTTTTTTTTTTTTTTTTTTTTTTXXXXXXXXXTTTT
    TTTTTTTTTTTTTTTTTTTTTXXXXXXXXXXXXTTTTTTTTTTTTTTTTT
    TTTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTTTTTTTT
    TTTTTTTTTTTTTTTTTXXXXXXXXXXXXXXXXXTTTTTTTTTTTTTTTT
    TTTTTTXXXXXXXXXXXXXXX

The length of your FASTA sequence and corresponding transmembrane sequence must be exactly the same.
Sequence Database

Your database of sequences should be in FASTA format. We ask that you submit a database because searching Swiss-Prot using SWAT takes about 30 minutes to an hour, and we are unable to support this on our server. If you desire to search against an entire database, please contact Phil Green (University of Washington) on how to obtain SWAT.

The PHAT matrices where constructed independent of SWAT. You can download the PHAT matrices as well as the BLOSUM matrices from us.

Questions or comments?
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