highlight residues in multiple alignment

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highlight residues in multiple alignment

Post by tevang » Tue Aug 11, 2009 4:50 am

Dear bioinformaticians,

does anyone know any multiple alignment editor where I can import a a list of residues to highlight, either in the form of a file or in batch mode? I have a MA of 52 proteins and need to highlight the residues of the binding cavity. You realize that doing this manually will be a torture.


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Post by jyaron » Tue Aug 11, 2009 4:57 am

I'm not a bioinformatician per se, but I know that Mekentosj has some great life science software (if you use a mac at least..). Check them out, let me know if it helps.
Experience: Cell Biology, Confocal Microscopy, Developmental Biology, Evolutionary Biology, Genetics, Genomics, Physiology

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Post by mith » Mon Aug 17, 2009 10:48 pm

err, do you already have the binding cavity residues defined? it sounds to me like you want to highlight residues but you also expect the proggie to know which parts of the linear seq correspond to the 3d shape.
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