Question: Multiple alignment filtering
0
gravatar for guillaume.rbt
4 weeks ago by
guillaume.rbt730
France
guillaume.rbt730 wrote:

Hi all,

I'm doing a multiple sequence alignment from protein sequences, and I would like to get only the varying positions, so that I can create sequence logo of variyng amino acids.

Would anybody a tool for multiple alignement that can output only variyng amino acids? Or maybe a tool that can filter a multiple alignment format, as clustal, to filter out all 100% identical amino acids between sequences?

Thanks

clustal multipe alignement • 116 views
ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by guillaume.rbt730
1

You can upload multiple sequence alignments to WebLogo to create a logo. If you are only looking for variable positions then it is opposite of what people are normally looking to do. Unless someone knows of an existing tool you may need to write something custom yourself.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by genomax74k

Thanks! The problem I've got is that I have long sequences (around 200 AA), with few variants (around 5). Hence if i submit the whole sequences to Weblogo the output it won't be readable, that's why I try to filter the multiple sequences alignment input.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by guillaume.rbt730

If you filter out only the variable positions, you’ll lose the positional information though, or are you not worried where the variants are?

ADD REPLYlink written 4 weeks ago by Joe14k

Indeed I will have to keep track of the positions for my figure.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by guillaume.rbt730

The scale will remain the same in that case. A 200 character web logo won't be readable, as you say, but there's no filtering you can do that will reduce the x axis if you're trying to keep the positions.

ADD REPLYlink written 4 weeks ago by Joe14k
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