[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


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