Question: Parsing Scop Pdb Files With Biopython
0
gravatar for Hpk
7.8 years ago by
Hpk60
Hpk60 wrote:

Hello,

How to parse SCOP25 PDB files (fasta sequences) with Biopython? Is it possible in Biopython? I need PDB seqres records and atom records.

astral-scopdom-seqres-all-1.75.fa. (URL of seqres)

astral-scopdom-atom-all-1.75.fa.(URL of PDB atom)

After parsing these files , I have to make an alignment of aminoacid residues from seqres and atom records.

pdb biopython • 2.5k views
ADD COMMENTlink modified 7.8 years ago • written 7.8 years ago by Hpk60
3

Could you clarify what you want to parse, e.g. Add the URL of a specific example? Biopython can parse FASTA and SCOP files.

ADD REPLYlink written 7.8 years ago by Peter5.8k
1

Sorry, missed out PdB as Neil points out. So, do you want to parse PDB (3D structure) format, FASTA (sequence) format or one of the various SCOP plain text files? Biopython should do all of those.

ADD REPLYlink written 7.8 years ago by Peter5.8k
1

In that case yes, Biopython will parse fasta: http://biopython.org/wiki/SeqIO. You should refine your question to state, specifically, what information you want from the files, if you want an answer.

ADD REPLYlink written 7.8 years ago by Neilfws48k

Yes, what format do you want to parse - PDB or fasta?

ADD REPLYlink written 7.8 years ago by Neilfws48k

Thanks for your comment. I want fasta sequence format

ADD REPLYlink written 7.8 years ago by Hpk60

@neil after parsing files, I have to make an alignment between seqres and atom records

ADD REPLYlink written 7.8 years ago by Hpk60
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1507 users visited in the last hour