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weblogo problem

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#1 alchemic



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Posted 24 September 2013 - 03:26 AM



I have a problem with generating weblogo from many sequences.


So I want to obtain a consensus sequence, but the problem is that I have more than 10000 sequences, and as far as I am know, it is not possible to do that with such huge amount of sequences usong WebLogo software.

Does anyone know a solution to my problem.

Or sobebody know the program in which I can introduced the numbers each nucleotide occur in each possition, and then create a weblogo (so the number or records will not be a problem any more).

User friendly interfence would be most desired as I am not a bioinformatics:))


Thanks for any replies.



#2 Felipillo



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Posted 11 October 2013 - 07:39 PM

Are you looking for motifs? Then you can use MEME you get a weblogo from each motif

Chance favors the prepared mind
Louis Pasteur.

#3 Soumble



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Posted 18 October 2014 - 02:13 AM

Are you looking for motifs? Then you can use MEME you get a weblogo from each motif

I need a  multiple alignment of a protein sequence from 81 different species. I want to use WebLogo as it gives result in precise way. But the problem is that these 81 sequences are not same in  length ranging from 730 to 830. WebLogo  does not accept these sequences and shows an error that sequence lengths are not equal. As you have been using WebLogo, can you tell me how to get rid of this problem? Is there any other soft ware that can accept sequences of varying lengths but gives result the same way WebLogo gives.

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