Question: Precomputed secondary structure prediction from sequence
2
gravatar for by0
6.1 years ago by
by0110
United Kingdom
by0110 wrote:

Hi, 

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). 

e.g. http://bioinf.cs.ucl.ac.uk/psipred/result/0fc9a438-c3d8-11e3-a745-00163e110593

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 • 2.3k views
ADD COMMENTlink modified 5.0 years ago by Biostar ♦♦ 20 • written 6.1 years ago by by0110
0
gravatar for User000
6.1 years ago by
User000370
User000370 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 6.1 years ago by User000370
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