Using Weblogo in Biopython

Question

[surka]

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?

Answer 1

[Peter]

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

[surka]

Hello Peter,

Sorry I never thanked you. I did not see this answer and assumed no one had responded to me.

Thank you for your advice.

[Peter]

It is easy to overlook an email. Did you solve your original problem?

[surka]

Yes, you were correct. I was having a massive brain dead moment...