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Old 04-30-2013, 05:58 PM   #1
vixensjlin
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Location: USA

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Question Could I make any RNA folding pages shown with pre-filled sequence in URL?

It is a odd question, I know, please let me explain it.

When you do a blast on line, there are two ways:

1. You go to NCBI Blast website, copy and paste a sequence and click "submit".

2. You can have a URL containing a sequence like the following one, the resulting page is pre-filled with sequence, No copy&paste required. You just need to click "submit"

http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?QUERY=ctgcagatcgtgcatagcgtcatgctagtcagtcga&AUTO_FORMAT=Fullauto&FORMAT_TYPE=HTML&PROGRAM=blastn&CLIENT=web&PAGE=Nucleotides


My question is: are there any RNA folding prediction sites can accept this kind of URL containing sequence? I couldn't find such info in mfold server or Vienna RNA webserver. Thanks a lot
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Old 04-30-2013, 06:19 PM   #2
GenoMax
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If your intent is to submit multiple jobs to a server why not acquire mfold software license (free for academics) and run the software locally?
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Old 04-30-2013, 09:40 PM   #3
vixensjlin
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Actually, I don't plan to submit many jobs simultaneously. Maybe several at most. Really appreciate if anybody know how to send sequence in URL for RNA folding estimation.
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Old 04-30-2013, 10:11 PM   #4
koustavpal
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Usually most rna folding servers have a limit to the length of sequence they will fold online, otherwise you can just download the vienna-rna package and just do it yourself, its a real cinch.

If you still want to do it online, as most servers usually use POST for fetching such data you can write a LWP or Curl script to do the same job for you.
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