Question: Precomputed secondary structure prediction from sequence
gravatar for by0
6.8 years ago by
United Kingdom
by0110 wrote:


Most services that predict secondary structure from sequence, such as psipred, have an online webserver or a program you'd have to run locally (which would take quite a bit for a whole proteome). 


I was wondering if anyone knew a reseource that had precomputed secondary structure predictions I can download for my proteome of choice (Yeast).

I would assume at least of one the services would run it (for example) on all of uniprot and provide the predictions in a database or flatfile.

Thanks in advance! 

helix secondary beta pdb 3d • 2.4k views
ADD COMMENTlink modified 5.6 years ago by Biostar ♦♦ 20 • written 6.8 years ago by by0110
gravatar for User000
6.8 years ago by
User000420 wrote:

I think one of the best solutions is to write a (Python) script yourself. SVM and PSIPRED prediction methods show higher Q3, you can base on algorithms of one of these two. Run PSI-BLAST of your fasta files against your DB to extract sequence profiles, then generate scoring matrices, do cross-validation and statistical validaton.

ADD COMMENTlink written 6.8 years ago by User000420
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