Clustalw2 Profile Alignment

Question

[monukmr98]

Hi all I am trying to align following using clustalw2 through command line:

(1) aligning profile (file1.aln) with the sequence (query.fasta). Command I used here is :

clustalw2 -SEQUENCES file1.aln query.fasta

(2) aligning first profile (file1.aln) with second profile (file2.aln). Command I used here is :

clustalw2 -PROFILE file1.aln file2.aln

But I have been unable to run commands successfully. Please suggest the needful syntax of commands in these two cases. Thanks in advance.

Monu kumar

[Niek De Klein]

What is not working? Are you getting an error, or is the result not as you expected?

Answer 1

[Andreas]

Hi,

the command-line usage for profile/profile and profile/sequence alignment is a bit counter-intuitive in ClustalW2. I think, In both cases you have to define one file as "profile1" and the other as "profile2". The boolean flag -sequences makes sure that sequences in "profile2" are aligned as single sequences and not as a profile. So here is what you have to do:

"1) aligning profile (file1.aln) with the sequence (query.fasta)"

Use clustalw2 -profile1=file1.aln -profile2=query.fasta -sequences

"(2) aligning first profile (file1.aln) with second profile (file2.aln)."

Use clustalw2 -profile1=file1.aln -profile2=file2.aln -sequences

Andreas