[Genome] fetching multiple genomic DNA sequences, and mRNAs

[Ewan Birney]

On 26 Jan 2008, at 01:13, Fungazid wrote:

> 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).
>

Just to let people know, at Ensembl each 2x genome gets its own
browser:

http://www.ensembl.org/Oryctolagus_cuniculus/index.html

which you can access via downloads or Perl API

http://www.ensembl.org/info/downloads/index.html

http://www.ensembl.org/info/using/api/index.html

Notice that we develop quite extensive ortholog and paralog
links between the gene sets on each genomes and the other
genomes, eg:

http://www.ensembl.org/Oryctolagus_cuniculus/genetreeview? 
db=core;gene=ENSOCUG00000001434


You can show external data on this browser as well, including
using UCSC style .wig and .bed files formatted for the UCSC
browser:

http://www.ensembl.org/info/using/external_data/index.html



This way you could display things on the Rabbit/Pika/elephant
genome on Ensembl as wished, as well as using the UCSC (or
Ensembl if you liked!) site for the less exotic genomes.


If you have any questions about this, do use the ensembl helpdesk,
helpdesk at ensembl.org




> 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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