Alignment of one sequence to a profile in CLUSTALW

ABC cdcer at hongkong.com
Mon Jun 30 07:20:29 EST 2003


I want to ask how to do the alignment of 1 sequence to a profile in
command mode Linux machine.

Assume test.fa stores 1 sequence, and pro1.aln stores the alignment of
10 sequences.

What I want to get is the alignment between test.fa and pro1.aln, also
the score of the particular sequence in test.fa to all 10 sequences in
pro1.aln.

I tried

> ./clustalw -profile1=t.aln -infile=5.fa

However, this does not work. Could any show me the way to do so?

Also, could I do it in batch. Meaning is if I have many single
sequence, e.g. from test1.fa to test1000.fa. Could I do it at a time
or write a program to do so? Any sample program for that?

Thanks a lot!!





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