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
>sp|P45090|ARTQ_HAEIN ARGININE TRANSPORT SYSTEM PERMEASE PROTEIN ARTQ - Haemophilus influenzae. XXXXXXXXXXXXTTTTTTTTTTTTTTTTTTTTTTTTTXXXXXXXXXTTTT TTTTTTTTTTTTTTTTTTTTTXXXXXXXXXXXXTTTTTTTTTTTTTTTTT TTTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTTTTTTTT TTTTTTTTTTTTTTTTTXXXXXXXXXXXXXXXXXTTTTTTTTTTTTTTTT TTTTTTXXXXXXXXXXXXXXXThe length of your FASTA sequence and corresponding transmembrane sequence must be exactly the same.
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.