How Can I Get Clustal Multiple Sequence Alignment Score?

Question

[Thaman]

I have run fasta file in http://www.ebi.ac.uk/Tools/clustalw2/index.html and got alignment file. Can anyone explain me how to get alignment score given in the right column of this output file -> http://pastebin.com/BhCMf34f

I want to generate following alignment score but couldn't make it.

Thanks in advance

[David W]

OK, I think you want to set the option -seqnos option to ON when you run clustal.

[David W]

Those aren't alignment scores, they're a counter for how far along the input sequence each break is. They are part of the Clustal format (The alignment score applies to the whole alignment, not one section of it).

[Istvan Albert]

Dear David, could you please enter your comment as an answer as well. That way people won't get discouraged when seeing an seemingly unanswered question.

[Nicojo]

I'm sorry Thaman, but what do you mean by "alignment score? The number you see at the end (is that what you refer to as the "right column"?) is simply the number of AA from the start of that sequence...

[Neilfws]

The numbers on the right side of that file are sequence positions for each sequence, not scores, unless I am missing something.

[Thaman]

Sorry i have misunderstood then, but output generated by the clustalw(.aln) doesn't have this record in the file. There are just sequence description and sequences in individual lines.

[Thaman]

@David w- Thanks that's what i want.

Answer 1

[David W]

As per Istvan's comment above I'll make my comment an answer:

The numbers in the right column are markers for how far along each aligned sequence each break in the file is.

To get them to show up in your clustal allignment you need to set the -seqnos option to ON