[Bioperl-l] Downloading annotated Gene nucleotide fasta files

[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-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at 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
Subject: Re: [Bioperl-l] Downloading annotated Gene nucleotide fasta files

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


On Fri, May 17, 2013 at 11:59 AM, Francisco J. Ossandón < fossandonc at hotmail.com> wrote:

> 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-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at 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
>
> 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 _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


--
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist) Department of Marine Sciences University of Georgia Athens, GA 30602-3636

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