Question: How To Find Disordered Residues From A Protein Sequence Using Biopython?
1
gravatar for Mkl
7.8 years ago by
Mkl100
Mkl100 wrote:

Hi,

I have a data set which contains 800 protein sequences. I would like to find disordered residues from each sequence. How to find disordered residues in Biopython?

ADD COMMENTlink modified 7.8 years ago by Lars Juhl Jensen11k • written 7.8 years ago by Mkl100
2

Could you expand your question with some example data? Biopython can read ASTRAL SCOP files and PDB files, so it should be possible. I don't (yet) understand what you are asking for exactly.

ADD REPLYlink written 7.8 years ago by Peter5.8k

Are you trying to read any disorder information in a PDB file explicitly, or infer/predict it from the structure?

ADD REPLYlink written 7.8 years ago by Peter5.8k

@peter I am trying to import ASTRAL SCOP original-style domain sequences, based on PDB SEQRES records and trying to find disordered residues from it using biopython. Is it possible in Biopython?

ADD REPLYlink written 7.8 years ago by Mkl100

How to parse Astral SCOP PDB files in Biopython?

ADD REPLYlink written 7.8 years ago by Mkl100

@peter I am trying to read PDB_Seqres sequences from SCOP.After this, I can do pairwise sequence alignment using clustalw with Biopython. gaps in the alignment denotes disordered residues.

ADD REPLYlink written 7.8 years ago by Mkl100
2
gravatar for Lars Juhl Jensen
7.8 years ago by
Copenhagen, Denmark
Lars Juhl Jensen11k wrote:

I think you are making a big mistake here by saying it must be done in BioPython. If you want to find disordered regions, you should use whichever prediction method that works the best. If that is not one that is integrated in BioPython, then so be it.

At the moment, I would use IUPred for this problem.

ADD COMMENTlink written 7.8 years ago by Lars Juhl Jensen11k
1

I would go a bit further than that Neil. Even if someone has implemented a disorder prediction algorithm in BioPython, you should not use it if it is not as good as the best available method. Your #1 criterion for selecting a method should be how well it does the job, not whether or not it has been implemented in BioPython.

ADD REPLYlink written 7.8 years ago by Lars Juhl Jensen11k
1

See comments on question itself - @mkl doesn't want to do the prediction in (Bio)python, rather parsing ASTRAL SCOP and/or PDB files for disorder information.

ADD REPLYlink written 7.8 years ago by Peter5.8k

Thank you for your answer.I know about the disorder prediction softwares.But I am trying to find disordered residues using Biopython.

ADD REPLYlink written 7.8 years ago by Mkl100

Question is: has someone implemented a disorder prediction algorithm for Biopython? If yes, all well and good. If not, as Lars says, then you should use the best available method.

ADD REPLYlink written 7.8 years ago by Neilfws48k

Completely agree Lars.

ADD REPLYlink written 7.8 years ago by Neilfws48k

Yes, I see that - but it was not clear from the original question at all.

ADD REPLYlink written 7.8 years ago by Lars Juhl Jensen11k
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