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How to get APIs or use web-based bioinformatics tools remotely.

Hi community,

Greetings!

I need your help in getting APIs or some way to use following web-based tools remotely (on linux server, docker image etc.)

  1. ARNOLD: Used to predict terminator regions in prokaryotes. Link: http://rssf.i2bc.paris-saclay.fr/toolbox/arnold/index.php#Results
  1. G2DPEPPER Promoter: Used to predict promoter regions in prokaryotes. Link: http://genome2d.molgenrug.nl/g2d_pepper_promoters.php#

Any kind of help will be much appreciated.

Thank you.

api arnold g2dpepper
• 1,619 views • link
updated by GenoMax GenoMax • written by Saransh • Saransh

some way to use following web-based tools remotely

As in without internet access?

Be careful to not swamp tool websites with a large amount of queries. Tools like these may be hosted by academic labs and are likely designed for low throughput use.

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written by GenoMax GenoMax

I mean, even with internet access, just want to refrain from going on website, pasting the query sequences and fetching the output. Some way through which I can just get it in some docker image form or API where I can provide my query sequences from the remote server and using internet it can provide me the results (Just like remote blast works).

• 0 views • link
written by Saransh • Saransh

just want to refrain from going on website

Solution Pierre posted below is going to hit the website just in a different way. Only way you may be able to do this is to install the software/database locally (if it is possible to do that).

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written by GenoMax GenoMax

1 answer

or some way to use

open the firefox" web developper tools ": https://developer.mozilla.org/en-US/docs/Learn/Common_questions/Tools_and_setup/What_are_browser_developer_tools

see what happens when you submit a FORM, see the POST parameters

use curl/wget to submit such form with your data

parse the HTML output

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Thanks a lot for your response. Will get back to you after trying this.

• 0 views • link
written by Saransh • Saransh

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