Creation of subset of diamond database

Question

[mark.bogen]

Hello, I am interested to perform a massive search with diamond program. I have a large protein database, but I am interesting to perform a search only on subset of it. I can not create a different database, because the set of the desired entries changes from run to run and the creation of database is computationally expensive. Is there any way to run my search against a subset of database restricted by a list of protein names. Thanks a lot,

Mark

Answer 1

[buchfink]

DIAMOND v2.0.8 now supports directly using BLAST database files, and also subsetting using --seqidlist. https://github.com/bbuchfink/diamond

[GenoMax]

buchfink : Not sure if DIAMOND has a tool post on Biostars. If not please consider creating one. Improvements such as these can then be directly announced in that thread to keep them visible.

Answer 2

[lieven.sterck]

With DIAMOND? I'm afraid not no (as far as I understood that kind of behaviour is not compatible with its DB/index structure)

but why not using 'normal' blast than? That does offer that kind of functionality (from version 5 DB onwards)

Answer 3

[buchfink]

It's not possible sorry, but it's a feature request I would consider useful. If you can wait 2-3 weeks I can make that feature available.

BTW you can speed up database creation by a lot by using the option --masking 0.

Benjamin

[mark.bogen]

Thanks a lot, I'll readily wait and also I'll try the --masking 0