Using Weblogo in Biopython
Hello,
I have a very silly question. I am attempting to create weblogos from large numbers of sequences (I have formatted them so they are all the same length).
I'm having a beginners issue, which is I'm not sure what format is required by the motifs module of Biopython.
At the moment I have a fasta file which has sequences such as:
>nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnGGGAAACGG
>nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnAGACAAAG
>nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnCTCCAAGG
>nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnGACAACAGG
>nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnGAGAAGG
>nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnCCAGGACA
>nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnGCTGCCTA
How should I change this so the motifs.create() command is happy with them?
1 answer
The main problem could simply be that you do NOT have a FASTA file. You have something like this:
>sequence1
>sequence2
...
You should have something like this:
>identifier1
sequence1
>identifier2
sequence2
...
Have you read the examples in the Biopython Tutorial yet? e.g. Creating a motif from instances http://biopython.org/DIST/docs/tutorial/Tutorial.html
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