Question: Bacterial genome collections in NCBI ftp
gravatar for niu2rseq
5.8 years ago by
United States
niu2rseq70 wrote:



I am trying to download the bacterial genome collection from NCBI ftp to blast against with my metatranscriptome data. 

I am now watching this folder:


I am not sure which file to download and no detail description was provided in the readme.txt. 

all.Glimmer3.tar.gz 119 MB 10/31/14, 7:08:00 AM
all.Prodigal.tar.gz 265 MB 10/31/14, 10:18:00 AM
all.asn.tar.gz 1.1 GB 10/31/14, 7:15:00 AM
all.faa.tar.gz 1.7 GB 10/31/14, 7:22:00 AM
all.ffn.tar.gz 2.5 GB 10/31/14, 7:30:00 AM
all.fna.tar.gz 2.7 GB 10/31/14, 8:09:00 AM
all.frn.tar.gz 8.8 MB 10/31/14, 8:52:00 AM
all.gbk.tar.gz 7.6 GB 10/31/14, 8:59:00 AM
all.gff.tar.gz 614 MB 10/31/14, 10:02:00 AM
all.ptt.tar.gz 210 MB 10/31/14, 10:05:00 AM
all.rnt.tar.gz 3.0 MB 10/31/14, 10:06:00 AM
all.rpt.tar.gz 413 kB 10/31/14, 10:07:00 AM
all.val.tar.gz 926 MB 10/31/14, 10:11:00 AM


I appreciate your comments and suggestions! Thank you!

metatranscriptome • 2.1k views
ADD COMMENTlink modified 5.8 years ago by RamRS28k • written 5.8 years ago by niu2rseq70
gravatar for RamRS
5.8 years ago by
Houston, TX
RamRS28k wrote:

These are different formats - GFF, FASTA, GenBank, etc. You could download the faa.gz archive and makeblastdb with it.

ADD COMMENTlink written 5.8 years ago by RamRS28k

Thank you RamRS! Two more questions:

1. Where can I find a detail description of the differences of these files? Like what are different between faa file and fna file?

2. For the bacterial_draft folder:

There is no collection file to contain everything, so what file I should download from each folder? 



ADD REPLYlink written 5.8 years ago by niu2rseq70

Googling "XYZ format" should help with the file formats. You might wanna make Qn 2 a new post.

ADD REPLYlink written 5.8 years ago by RamRS28k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1158 users visited in the last hour