Predict protein secondary structure from alignment

Question

[chaperoneline]

Dear all,

I want to predict the secondary structure using MSA as input.

I looked up Jpred4, which can use both sequence fasta or alignment in fasta format as input. However, it only provides a RESTful API for users to submit the jobs to their server, and I would like to work locally instead.

PSIPRED is another option, but it seems to not accept B in the amino acid code...

Do you have any other recommendation?

[jgreener]

Does B mean either aspartic acid or asparagine? If so, you could replace B with D or N and run through PSIPRED.

Answer 1

[Kevin Blighe]

You may try one or more of the tools at the Protein Model Portal

Kevin

Answer 2

[AsoInfo]

You can use JPred and also you can find the list of protein secondary structure prediction tools: https://molbiol-tools.ca/Protein_secondary_structure.htm