i have a fasta file of yeast orfs (from the SGD database) and i need to find out(predicted) secondary structure/classification for all of them (so ~6K queries and doing this by hand on numerous available websites is not an option). is CATH database a place that can give me this info? (so far i struggle to recover anything that can help me from the website but perhaps i am missing something), if not what's the best way/software to go about it? surely, these predictions have been done before and there is a databse somewhere -- yeast is too much of an important organism, with a lot of information about its genome.
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$\begingroup$ Lot of resources are available online, choose depending on your requirement and protein of interest. $\endgroup$– DexterCommented Nov 6, 2015 at 13:52
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$\begingroup$ @Dexter, thank you. i am well aware of this site and others but i need the procedure automated: i have ~6k ORFs and i need to run all of them through the algorithm to obtain secondary structure. $\endgroup$– stas gCommented Nov 6, 2015 at 13:55
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$\begingroup$ Then you need little bit programming with server queries. Alternately, search for server which accept batch sequences. $\endgroup$– DexterCommented Nov 6, 2015 at 14:04
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$\begingroup$ @Dexter unfortunately this is not something i am able to do, so i was more after either a piece of code (R/python) or a relatively easy to use software. i am struggling with installing and running s2D (whose server version i've tried and approved) at the moment and it's a nightmare. $\endgroup$– stas gCommented Nov 6, 2015 at 14:15
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2 Answers
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From comments I understood that you need to predictions in bulk. You can use API based system of JPred. They allow you to submit more than 1000 jobs per user per day. You can go through instructions step by step from their documentation. It looks simple !
Another hit I got while searching is Phyre2. I am sure there are many such servers.
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$\begingroup$ Phyre2 took a non-trivial amount of time for me to get a model back. I don't know if their batch processing is any quicker, though. $\endgroup$ Commented Nov 6, 2015 at 18:57
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$\begingroup$ @canadianer I haven't checked any of these sites. API integration sounds interesting. My personal choice will be submit to ExPASY server through python queries but OP is not (or don't want to be) a programmer I guess. $\endgroup$– DexterCommented Nov 7, 2015 at 4:29
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$\begingroup$ @Dexter like you said JPred was very easy to set up and use, thank you again. and i am programming myself, however i am not very experienced in python and i don't have much time to learn how to submit queries etc in python at the moment $\endgroup$– stas gCommented Nov 10, 2015 at 16:00
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$\begingroup$ No problem. Go with whatever you find easier. At the end only thing matter is to get your job done. $\endgroup$– DexterCommented Nov 10, 2015 at 16:27
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in addition to Dexter's answer i found that the s2D does exactly what i need. setting up might be a bit tricky and is certainly more involved than setting JPred up but using it is easy and the output is in a nicer format.