How to include NCBI blastp while making an online database?
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7 months ago
ThulasiS ▴ 70

Hi

I am creating a database of orthologues and would like to add option blastp to my database web page. How we can integrate blastp in this scenario. Is there any python module available to do so? I don't have experience in database designing.

Thank you in advance

python database NCBI • 274 views
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7 months ago
Carambakaracho ★ 2.7k

https://biopython.org/docs/dev/api/Bio.Blast.Applications.html

EDIT: don't use this

I don't know what you plan, but be aware that might be a substantial effort, though not on the database side. From the database, all you need is keep the index in the background up to date with the database, in case the data might change. If the data remains static, that's less of an issue.

Fmpov, the major effort is to design the web entrypoint. blast is only available as commandline tool so you need to wrap the system call, the input parameters, parse the output and display it correctly.

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Apologies for the link, I didn't read the text properly now spotted the OBSOLETE mark. This is their current recommendation and probably the way I had done it, too.

We have decided to remove this module in future, and instead recommend building your command and invoking it via the subprocess module directly.

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Thank you for the information. We want to execute blastp for users with our available sequence as blast database; something like this http://www.mgc.ac.cn/VFs/blast/blast.html. But I am not sure how to integrate. Will it be done by wrapping the system call?

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