[Genome] fetching multiple genomic DNA sequences, and mRNAs

[Fungazid]

Good {evening,morning} Ann and Hiram, 

The solution of creating a custom track and then being
redirected to the “table browser” is useful.  As
mentioned it doesn’t work for all species
(especially not for the more exotic guys). I’m not
sure how can I process data from the huge
scaffold.fa.gz  files (maybe with Bioperl, but not so
easily).

Thanks,
Avi

--- Ann Zweig <ann at soe.ucsc.edu> wrote:

> Hello Fungazid,
> 
> 	In addition to what my colleague, Hiram, has said,
> I would like to add 
> the following.  The rabbit and elephant browsers
> have not been built for 
> the public website.  But the sequence is available
> from our download 
> server:
>
http://hgdownload.cse.ucsc.edu/downloads.html#sequence_only
> 
> 	You will also be able to extract sequence for the
> rabbit and elephant 
> using the Conservation track on the latest human
> browser (hg18) and 
> associated MAF files: 
>
http://hgdownload.cse.ucsc.edu/goldenPath/hg18/multiz28way/maf/
> 
> 
> Regards,
> 
> ----------
> Ann Zweig
> UCSC Genome Bioinformatics Group
> http://genome.ucsc.edu
> 
> 
> 
> Hiram Clawson wrote:
> > Good Afternoon Fungazid:
> > 
> > Please see similar answered question earlier today
> on
> > the genome email list:
> >
>
http://www.soe.ucsc.edu/pipermail/genome/2008-January/015411.html
> > 
> > --Hiram
> > 
> > Fungazid wrote:
> >> Hello,
> >>
> >> I would like to fetch multiple genomic sequences
> and
> >> mRNA sequences of rabbit (orycun1), elephants
> >> (loxafr1), and other guys. I am looking for a web
> >> interface that gets a table of loci or scaffolds
> or
> >> genes, and returns the sequences (or some really
> >> reliable windows Perl API, that fetch it). I am
> also
> >> interested in fetching all homologous genes mRNA
> >> sequences for a given gene.
> >>
> >> Thank you for your help
> > _______________________________________________
> > Genome maillist  -  Genome at soe.ucsc.edu
> > http://www.soe.ucsc.edu/mailman/listinfo/genome
> 



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