Question

NT database update (number of files)

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4.7 years ago

anasofiamoreira94 ▴ 80

We started to perform a blast analysis with the v5 version, but we detected a problem with this DB. So we downloaded the v4. However, with this version I can no longer filter my blast to some ID seqs. I have some questions regarding blastDB: 1- If I want to download, again, the most recent version of nt DB, I should download those present in here: https://ftp.ncbi.nlm.nih.gov/blast/db/. However, to nt database I only get 22 files, is this normal? Cause the previous version of v5 add about 60 files. Thanks

nt blastn ãlignment • 2.7k views

ADD COMMENT • link updated 4.7 years ago by GenoMax 147k • written 4.7 years ago by anasofiamoreira94 ▴ 80

score 3 · Accepted Answer · 2020-03-05

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4.7 years ago

GenoMax 147k

Yes the current db at FTP link seems to have 22 files for nt. That said there have been rare instances when the database files on FTP link have been incomplete. I suggest that you check in a day or so to see if that number goes back up. You could email blast help but before they get around to responding the problem may be fixed.

Best option to deal with blast database downloads is to use the update_blastdb.pl script that is included with blast+ package.

Edit: Emailed blast product manager at NCBI. Will post an update once if I hear back.

ADD COMMENT • link 4.7 years ago by GenoMax 147k

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You may notice, that current nt.xx.tar.gz has almost 3GB which is about 3 times the size of the old nt part.

ADD REPLY • link 4.7 years ago by massa.kassa.sc3na ▴ 630

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NCBI confirmed that this is indeed the reason for smaller number of files.

ADD REPLY • link 4.7 years ago by GenoMax 147k

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Thank you so much for the help genomax

ADD REPLY • link 4.7 years ago by anasofiamoreira94 ▴ 80