Question

How to use stringdb offline for finding interactions between 4000 protein sequences?

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6.7 years ago

Dattatray Mongad ▴ 370

Web server limits the search for more sequences. I am new to this database. I wanted to predict protein-protein interactions between around 4000 protein sequences which are predicted by GenMark.

sequence • 1.5k views

ADD COMMENT • link updated 6.7 years ago by GenoMax 141k • written 6.7 years ago by Dattatray Mongad ▴ 370

score 0 · Answer 1 · 2017-08-18

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6.7 years ago

GenoMax 141k

Refer to this thread for downloading STRING data and other things: String Database download data including interactions

ADD COMMENT • link 6.7 years ago by GenoMax 141k

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I have downloaded interactions. Now I have sequences of about 4-5K proteins. I want to scan all those sequences and predict a PPI. As the webservice of stringDB does not support such large size of input, I have to do it offline. Just simply my question is ------------ How to use PPI data to scan against protein sequences?

ADD REPLY • link 6.7 years ago by Dattatray Mongad ▴ 370