Question: Bacterial genome collections in NCBI ftp
0
gravatar for niu2rseq
5.0 years ago by
niu2rseq70
United States
niu2rseq70 wrote:

Hi,

 

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:

ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/

 

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 • 2.0k views
ADD COMMENTlink modified 5.0 years ago by RamRS24k • written 5.0 years ago by niu2rseq70
1
gravatar for RamRS
5.0 years ago by
RamRS24k
Houston, TX
RamRS24k wrote:

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

ADD COMMENTlink written 5.0 years ago by RamRS24k

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: ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria_DRAFT/

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

 

Thanks!

ADD REPLYlink written 5.0 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 5.0 years ago by RamRS24k
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