Entering edit mode
13.0 years ago
Hpk
▴
60
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.
Could you clarify what you want to parse, e.g. Add the URL of a specific example? Biopython can parse FASTA and SCOP files.
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.
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.
Yes, what format do you want to parse - PDB or fasta?
Thanks for your comment. I want fasta sequence format
@neil after parsing files, I have to make an alignment between seqres and atom records