Question: How Can I Get Clustal Multiple Sequence Alignment Score?
3
gravatar for Thaman
10.8 years ago by
Thaman3.3k
Finland
Thaman3.3k wrote:

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

alignment scoring clustalw • 6.1k views
ADD COMMENTlink modified 10.8 years ago by David W4.8k • written 10.8 years ago by Thaman3.3k
3

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

ADD REPLYlink modified 18 months ago by Ram32k • written 10.8 years ago by David W4.8k
2

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).

ADD REPLYlink written 10.8 years ago by David W4.8k
1

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.

ADD REPLYlink written 10.8 years ago by Istvan Albert ♦♦ 86k

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...

ADD REPLYlink written 10.8 years ago by Nicojo1.1k

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

ADD REPLYlink written 10.8 years ago by Neilfws49k

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.

ADD REPLYlink written 10.8 years ago by Thaman3.3k

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

ADD REPLYlink written 10.8 years ago by Thaman3.3k
6
gravatar for David W
10.8 years ago by
David W4.8k
New Zealand
David W4.8k wrote:

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

ADD COMMENTlink written 10.8 years ago by David W4.8k
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