Sequence Comparison using Bipartite Scheme with SWAT

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Sequence Comparison for Transmembrane Sequences

The user specifies the regions he considers to be transmembrane in the sequence, and then chooses the substitution scoring matrices to be used on nontransmembrane and transmembrane regions.
The PHAT matrix (Ng, Henikoff, Henikoff, 2000) is built from predicted hydrophobic and transmembrane regions and performs significantly better at database searching on transmembrane regions than any previously published matrix. (More on PHAT matrices). Users may see improved alignment using the PHAT matrix on transmembrane regions rather than general matrices.
SWAT (Green, P. University of Washington), a Smith-Waterman alignment tool, will be used to align your sequences. (Details)
Default is BLOSUM 62 (Henikoff & Henikoff, 1992) on nontransmembrane regions and PHAT 75/73 (Ng, Henikoff, Henikoff, 2000) on transmembrane regions.
We have also included BLOSUM 55, which has similar entropy to PHAT 75/73, and JTT-modified PAM (Jones, Taylor, Thornton, 1992) and the JTT transmembrane matrix (Jones, Taylor, Thornton, 1994)

Select the matrix for nontransmembrane regions:

Select the matrix for transmembrane regions:

Enter the name of the file containing your sequence in FASTA format:
-or-
Enter the sequence in FASTA format here:

Enter the name of the file containing transmembrane regions in corresponding FASTA-like format (Example) (Transmembrane Prediction Websites)
-or-
Enter the corresponding transmembrane regions in FASTA-like format here (Example) (Transmembrane Prediction Websites)

Enter the name of a file containing your database sequences:
-or-
Enter your database sequences in FASTA format):

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