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Blastx versus nr?

Hi everybody,

I want to perform a blastx versus nr locally for 2200 sequences, it is normal to take long long time? expected time to make it is about 800 hours!!

Somebody has had the same problem?

Any suggestions?

blast blastx long_time computing_hours
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updated by Biostar Biostar • written by Buffo Buffo

Would depend on length of the sequences and power of the computer infrastructure you have available locally. Still 800 h sounds a bit long.

I second suggestion for DIAMOND, but two critical things to keep in mind. You will need to create an index for nr with DIAMOND. You would also need a substantial amount of RAM for DIAMOND searches (if I recollect right ~60-80G).

• 0 views • link
written by GenoMax GenoMax

Thanks, I had heard about that, but I was looking for a suitable solution with blast, I will try diamond.

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written by Buffo Buffo

2 answers

I'd use DIAMOND instead of BLASTX as it's much faster than standard BLAST.

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written by Sej Modha Sej Modha

I use Plast when Blast is too slow for me. It's also much faster especially if you decrease the seed-use ratio a bit.

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written by Jake Warner Jake Warner

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