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Comparison of NCBI Full NR and NR.00

Hi folks,

I'm wondering if I only use nr.00 to compute the PSSM matrix, will the results be much different than if I compute it with the full nr database?

I have lots of sequences need to be computed and using full nr database do require a long time. so I am wondering if it is okay to only use nr.00 to compute the PSSM.

ncbi pssm blast non-redundant
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written by Allie • Allie

1 answer

nr.00 is not a database. It is only the first part of the whole nr, which last time I checked had something like 60 parts. So you would be searching against a random 1/60th of the whole database, which is almost guaranteed not be optimal even though it would be faster.

If you want to do a proper search against a reduced database, I suggest UniRef50:

https://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref50/

You want a file ending in .fasta.gz and you will need to create indexes for BLAST. If I remember correctly, this database is about 1/3 of regular nr but it still includes representatives of all sequences.

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written by Mensur Dlakic Mensur Dlakic

Many thanks Mensur!

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written by Allie • Allie

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