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Bacterial genome collections in NCBI ftp

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
• 3,405 views • link
updated by Ram Ram • written by niu2rseq niu2rseq

1 answer

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

• 0 views • link
written by Ram Ram

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!

• 0 views • link
updated by Ram Ram • written by niu2rseq niu2rseq

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

• 0 views • link
written by Ram Ram

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