Biopython - Extracting Nucleotide Frequency On Aligned Sequences
2
1
Entering edit mode
11.5 years ago

I was wondering how I might be able to use the BioPython package to extract nucleotide frequencies over an aligned set of sequences. Does anybody know how I might be able to do this? I am assuming that I have aligned sequences, including the appropriate spacers at places where base pair deletions have occurred.

Is there a single function in the BioPython package that allows me to do that? I've tried browsing through the API, but I haven't been able to find anything. (It might be I'm not looking at it correctly, or that the terminology used is different, perhaps?)

nucleotide-frequency alignment biopython • 5.0k views
ADD COMMENT
2
Entering edit mode
11.5 years ago
Medhat 9.8k

did you tried this Bio.Align.AlignInfo.Summary Calculate summary info about the alignment.

This class should be used to caclculate information summarizing the results of an alignment. This may either be straight consensus info or more complicated things.

ADD COMMENT
1
Entering edit mode
11.5 years ago
cts ★ 1.7k

I was trying to do the same thing recently, and like you couldn't find anything. In the end I used pycogent which has quite a rich API for alignments. Take a look at this page for some toy examples of doing this.

ADD COMMENT

Login before adding your answer.

Traffic: 2442 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6