[Genome] exons and a number of adjacent basepairs

[Brooke Rhead]

Hello Frode,

The Table Browser has several options for retrieving and formatting 
sequence that will fit your needs.  To use it, follow the "Tables" link 
in the blue bar at the top of the page, and select the clade, genome, 
and assembly you wish to use.  Select "group: Genes and Gene Prediction 
Tracks".  For "track" you will need to decide which gene set you wish to 
use.  If you don't already have a gene track in mind, you can read about 
each one by clicking on the track name on the main browser page (the 
blue links above the drop-down boxes that control visibility).

Once you have made the selections above, you can either enter a 
particular gene name in the position box (and select "region: position") 
or paste a list of gene identifiers to use (and select "region: 
genome").  Then choose "output format: sequence".  If you want to 
download the results to your computer, enter a filename for "output 
file".  Now hit "get output".  On the next page, choose "genomic" 
sequence type and hit submit.

Now you can choose to output only the exon sequences.  Be sure to select 
the "One FASTA record per region (exon, intron, etc.)" option.  Here you 
can also choose to add extra bases upstream and downstream of each exon. 
  When you have finished making your selections, hit "get sequence". 
You should get a file containing sequence for each exon.

I hope this information is helpful.  Please let us know if we can 
clarify any of these instructions, or if you have further questions.

--
Brooke Rhead
UCSC Genome Bioinformatics Group



Lingaas Frode wrote:
> Hi,
> If I want to study the genomic organization of a gene, is it possible to
> get out a file containing 
> 
> a) separate sequences/files of each exon, or better one file containing
> separate/individual exon-information of all the exons
> 
> b) alternatively a file containing separate exon-sequences with a number
> of basepairs (optional, eg 300bp) of additional sequence on each side of
> each of the exons.
> 
> Thanks.
> 
> Best regards
> 
> 
> Frode Lingaas
> --------------------------------------------------------------
> Frode Lingaas
> professor, Section of Genetics,
> Norwegian School of Veterinary Science
> PO.Box  8146 Dep.
> N-0033 Oslo
> Norway
> frode.lingaas at veths.no
> T: +4722964780
> 
> 
> 
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