Two-sequence alignment server (lalign and prss)

This server uses William Pearson's lalign and prss programs. The lalign program implements the algorithm of Huang and Miller, published in Adv. Appl. Math. (1991) 12:337-357. The principles of prss have been published in: Pearson and Lipman, PNAS (1988) 85:2444-2448, and Pearson (Meth. Enz. 183:63-98).

These programs are part of the FASTA package of sequence analysis program. The complete package is available by anonymous ftp from ftp.virginia.edu.

Usage: Paste your two sequences in one of the supported formats into the sequence fields below , select the program you want to run and finally press the "Run" button.
Make sure that both format buttons (next to the sequence fields) show the correct formats
substitution matrix
number of reported sub-alignments (lalign only).
number of 'shufflings'(prss only).
shuffling window (prss only).

First sequence title (optional):
1st Query sequence (see above for valid formats):

Second sequence title (optional):
2nd Query sequence (see above for valid formats):

make alignment (use lalign)
calculate significance (use prss)

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