Question: Using Weblogo in Biopython
0
gravatar for surka
5.5 years ago by
surka0
United Kingdom
surka0 wrote:

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?

biopython weblogo • 3.3k views
ADD COMMENTlink modified 5.5 years ago by Peter5.8k • written 5.5 years ago by surka0
1
gravatar for Peter
5.5 years ago by
Peter5.8k
Scotland, UK
Peter5.8k wrote:

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

ADD COMMENTlink written 5.5 years ago by Peter5.8k

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. 

ADD REPLYlink written 5.4 years ago by surka0

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

ADD REPLYlink written 5.4 years ago by Peter5.8k

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

ADD REPLYlink written 5.3 years ago by surka0
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