Re: [gaggle-discuss] Visualization nucleotide sequence

[Christopher Bare]

On Thu, Jul 26, 2012 at 10:20 AM, Liliane <lilian...@gmail.com> wrote:

Hi,

I am using the genome browser in my project and I would like to know if exists any function that allows visualize the nucleotides sequence instead of coordinate axis. A friend told this function exists, but I don't found...

Thanks for help.

[]s.

Hi Liliane,

If you have a recent version of GGB, you'll have a sequence menu item in the top menu bar. Under that, there are two options. Import FASTA will read FASTA files, which should correspond exactly to the genomic coordinates used to define the chromosomes / plasmids / etc.

We haven't added in an option to view the sequence in the main window. You can high-light a region and show its sequence in the sequence menu.

Thanks,

- Chris

[Salvanha, D M]

Dear Liliane,

I hope I can help you out about your sequence Issues.

After importing all fasta files from your organism (menu Sequence > Import Fasta to the current DataSet) there are 2 ways you can get nucleotide sequence automatically.

1st. way - Highlight a desired "range of tracks" and  Add a Bookmark (Crtl+B) (nt sequence must show up inside the Sequence textField)

2nd. way - Menu Sequence > Show Sequence (Alt + S ) you can create a query that fits your constraints.

Hope this is what you are looking for !

Let me know if you have any other issue I can help you.

Cheers.,
--------------------------------------------------------------------
 Diego M Salvanha

Doutorando em Bioinformática - Programa interunidades em Bioinformática

Universidade de São Paulo / FFCLRP-USP

Departamento de Computação e Matemática - DCM 

Integrante do LabPIB - Laboratorio de Processamento de Informação Biologica

Linux user # 504787
P Antes de imprimir, pense no AQUECIMENTO GLOBAL.

http://labpib.fmrp.usp.br

On Thu, Jul 26, 2012 at 2:20 PM, Liliane <lilian...@gmail.com> wrote:

Hi,

I am using the genome browser in my project and I would like to know if exists any function that allows visualize the nucleotides sequence instead of coordinate axis. A friend told this function exists, but I don't found...

Thanks for help.

[]s.

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