[Bioperl-l] Downloading annotated Gene nucleotide fasta files

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