Documentation about Bio. Site.search_pwm method in BioPython

Hi everyone,

It's my first time with biopython, and I want to use a method described in a paper I'm interested in ( Emily Clough et al 2014) as the Bio. Site.search_pwm method.

I was looking directly in the Biopython documentation : http://biopython.org/DIST/docs/tutorial/Tutorial.html http://biopython.org/DIST/docs/api/

but I'm still unable to find where the documentation for Bio.site is. It's not even in the api documentation.

Does this module still exists ? Any idea about it ?

Thanks for your help !

Cheers,

Roxane

biopython

• 1,989 views • link

updated 10.1 years ago by samuelmiver

• written 10.1 years ago by Rox

1 answer

Here you have a very well documented example in GitHub that uses the method you are looking for:

https://github.com/bigwiv/Biopython-cn/blob/master/en/chr14.rst

• 1 views • link

written 10.1 years ago by samuelmiver

Well, thanks ! I think that's exactly what I was looking for ! Have a nice day :)

• 1 views • link

written 10.1 years ago by Rox

More posts like this

Biopython separate gap score functions for border/internal gaps
written 4.7 years ago by Tios •

Hi, I would like to define different gap score functions for left/right/internal gaps in Biopython. After reading the documentation (http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec101, section 6.6.2.5), I found out …
How to write a BGZF file with Biopython?
written 6.8 years ago by mrals89

Hi everyone, I've read the documentation for [`Bio.bgzf`](https://biopython.org/DIST/docs/api/Bio.bgzf-module.html) and I'm sufficiently confused by it. To create an example bgzf file, I've tried the following. The …
How do I download and install DSSP?
written 7.8 years ago by westin.kosater •

I am looking through the Biopython Tutorial and Cookbook (http://biopython.org/DIST/docs/tutorial/Tutorial.html) and in order to look at DSSP files with biopython, I need to obtain a …
AttributeError: 'Hit' object has no attribute 'sacc_ver'
written 8.8 years ago by bioinfoSeeker •

Hi, I am trying to write a script to parse and summarize the ncbi web blast output (14 columns). I am using biopython searchIO on …
Connect to JASPAR database with biopython
written 10.0 years ago by themantalope •

Hi All, I've done an analysis where I've identified DNA motifs and mapped them to known TF-binding motifs within the JASPAR database. Now, I need …
amino acid weight confusion
written 11.8 years ago by jsbrava •

I'm taking a class that uses stepic.org. We're given a list of amino acid weights: https://stepic.org/lesson/CS-Generating-the-Theoretical-Spectrum-of-a-Peptide-4912/step/1 For example, it gives the weight of A as …
How To Differentiate Files With One Record From Files With Multiple Records?
written 12.6 years ago by Cako Fuentes •

I'm working with biopython, python, and gtk to create a program to load files of bioinformatic interest. These files have multiple sequence in them http://biopython.org/DIST/docs/tutorial/examples/ls_orchid.gbk …
Java Equivalent Of Biopython'S Ncbixml Parser
written 13.1 years ago by aliahmadvand2004 •

I'm looking for a method similar to Biopython's parse method of NCBIXML in java this is the parse method <a href='http://biopython.org/DIST/docs/api/Bio.Blast.NCBIXML-module.html#parse'>http://biopython.org/DIST/docs/api/Bio.Blast.NCBIXML-module.html#parse</a>
Update Biopython'S Seqrecords?
written 13.5 years ago by biocyberman

I looked at the documentation here: <a href="http://biopython.org/wiki/SeqRecord">http://biopython.org/wiki/SeqRecord</a> , but I did not find any information or methods to update properties of SeqRecords. I want …
How To Parse Psiblast Results Using Biopython And Blast-2.2.24+?
written 15.9 years ago by Niek De Klein

I'm trying to run a PSIBlast program which selects certain sequences out at every round before it does the next iteration. For this I need …