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Clustalw Multiple Sequence Alignment Parsing

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
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updated by Biostar Biostar • written by Thaman Thaman

1 answer

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.

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updated by Ram Ram • written by Giovanni M Dall'Olio Giovanni M Dall'Olio

What you mean put each sequence on a single line?

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written by Thaman Thaman

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