Question: Clustalw Multiple Sequence Alignment Parsing
1
gravatar for Thaman
8.8 years ago by
Thaman3.2k
Finland
Thaman3.2k wrote:

I am updating my previous question due to serious typo.

I have got alignment file generated from clustalw and i want to parse output like http://www.ebi.ac.uk/Tools/clustalw2/

I am using python with html embedded in it.

Main objective is to present alignment in clear and concise way looking like this and my output look like this which is not clear not.

And I want to know what are clustal alignment record attributes

parsing • 3.0k views
ADD COMMENTlink modified 6 months ago by RamRS20k • written 8.8 years ago by Thaman3.2k
1
gravatar for Giovanni M Dall'Olio
8.8 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

Note that if you follow the suggestion of embedding a jalview applet as explained here, you will be able to do what you want in 5 minutes and have a nice visualization as a plus.

Otherwise, you can parse clustalw with python using biopython. To visualize it better, you should put each sequence on a single line, without wrapping them.

ADD COMMENTlink written 8.8 years ago by Giovanni M Dall'Olio26k

What you mean put each sequence on a single line?

ADD REPLYlink written 8.8 years ago by Thaman3.2k
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