[Bioperl-l] Downloading annotated Gene nucleotide fasta files

[shalabh sharma]

HI,
First of all i am really sorry for sending this mail here,
i am not sure if this is the right forum. I know lot of people work on
similar stuff.
I wrote to NCBI but nobody replied.

Actually i am looking for all bacterial/microbial gene annotation
nucleotide fasta files.
Does anyone knows where to download these kind of files.
I tried *ffn files but they are not annotated.
Or is there any module in bioperl that i can use ?
I would really appreciate your help.

Thanks
Shalabh

--
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636
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[Francisco J. Ossandón]

Hi,
You can get the annotations from here:
ftp://ftp.ncbi.nih.gov/genomes/Bacteria/

The ".ffn" are the genes nucleotide fasta files but it does not show the
product name, on the other hand the ".faa" are the genes aminoacid fasta
files and shows the product name, but if you want both product and
nucleotide is much better to use the Genbank ".gbk" files that contains the
complete data and you can parse it easily using BioPerl to obtain all genes,
and then print the /protein_id, /product, and the nucleotide sequences in a
new fasta file. Check these to see how to do it:
http://www.bioperl.org/wiki/HOWTO:SeqIO
http://www.bioperl.org/wiki/HOWTO:Feature-Annotation

Cheers,

Francisco J. Ossandon

-----Mensaje original-----
De: bioperl-...@lists.open-bio.org
[mailto:bioperl-...@lists.open-bio.org] En nombre de shalabh sharma
Enviado el: viernes, 17 de mayo de 2013 10:55
Para: bioperl-l
Asunto: [Bioperl-l] Downloading annotated Gene nucleotide fasta files

[shalabh sharma]

Hey Francisco,
Thanks a lot. Basically i just wanted gene nucleotide fasta
files with GI numbers.
I think i will have to parse it from gbk files.

-Shalabh

[shalabh sharma]

Thanks Russell,
Actually i wanted all the Bacterial gene
nucleotide files, so i parsed it from *gbk. But yes these files might help
me for my other parts of my work.

Thanks
Shalabh


On Sun, May 19, 2013 at 3:26 PM, Smithies, Russell <
Russell....@agresearch.co.nz> wrote:

> Another option that I've used before is to download the gene2accession,
> gene2refseq, and gene_info files from here
> ftp://ftp.ncbi.nih.gov/gene/DATA/ then parse out the data you require.
> It might work for you?
>
> --Russell

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[Smithies, Russell]

Another option that I've used before is to download the gene2accession, gene2refseq, and gene_info files from here ftp://ftp.ncbi.nih.gov/gene/DATA/ then parse out the data you require.
It might work for you?

--Russell

-----Original Message-----
From: bioperl-...@lists.open-bio.org [mailto:bioperl-...@lists.open-bio.org] On Behalf Of shalabh sharma
Sent: Saturday, 18 May 2013 4:26 a.m.
To: Francisco J. Ossandón
Cc: bioperl-l

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