Downloading Blast Database(nr)

Question

[Sumit]

Recently I have downloaded the nr database from ncbi website (ftp://ftp.ncbi.nlm.nih.gov/blast/db/). Although, in the readme file it is instructed that the pre-formatted database must be downloaded with update_blastdb.pl script, I downloaded all the 50 files nr.*.gz one by one manually. Can it cause a problem in calculating PSSM matrix using this database?

Secondly, while downloading the database, there was an update in the database files.So some of the files I downloaded are of different updates?As they take a long time, I could not download them all under same update. Will it cause a problem?

Thank you.

Answer 1

[Sej Modha]

If you are using the latest version of the update_blastdb.pl there should not be any problems. You could use decompress option to download the uncompressed version of the databases and in case there is a firewall issue it is advisable to use --passive option to overcome that.

update_blastdb.pl --passive --decompress nr

[GenoMax]

Based on the original post the constraint appears to be available network bandwidth so trying to download uncompressed versions may make problem worse.

Answer 2

[GenoMax]

If I recollect right the update_blastdb script is meant for sys admins and such who regularly download updates to keep local copies of indexes fresh. Manually downloading files should not cause any problems. That said, you could download the fasta format file from this directory and build the database locally (still going to be a big download and a big job to build the indexes) but at least you can be sure that the database indexes will be consistent.

[Sumit]

Thanks for your reply. I did not know that the database can be built in this way. I am going to give it a try.