Hello Richard,
You can find the information you are looking for in the details pages of
the EvoFold and Conservation tracks. You can get to these pages by
clicking on the blue/gray bar to the left of these tracks in the main
display or on the link above the pulldown for each track.
Note that the EvoFold track was generated using dm2 not dm3. The details
on the methods used to generate the EvoFold track from the details page
are as follows:
The predictions for this track were based on the conserved elements of a
12-way Drosophila alignment of the D. melanogaster (dm2), D. simulans
(droSim1), D. sechellia (droSec1), D. yakuba (droYak2), D. erecta
(droEre2), D. ananassae (droAna3), D. pseudoobscura (dp4), D. persimilis
(droPer1), D. willistoni (droWil1), D. virilis (droVir3), D. mojavensis
(droMoj3), and D. grimshawi (droGri2) assemblies. The 12-way Drosophila
alignment was extracted from a 15-way insect alignment, which is the one
displayed in the Conservation track.
And the phylogenetic tree used for this track can be found on the
Conservation track details page:
(((((((((dm2 (droSim1 droSec1))
(droYak2 droEre2)) droAna3)
(dp4 droPer1)) droWil1)
((droVir3 droMoj3) droGri2))
anoGam1) apiMel2) triCas2)
Hopefully this information was helpful and answers your question. If you
have further questions or require clarification feel free to contact the
mailing list at [EMAIL PROTECTED]
Best regards,
Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu
Richard Lin Zhou wrote:
> Hi Brooke,
>
> Thanks for your reply.
>
> Actually I was wondering whether you have performed evofold based on the
> alignment of 14 species in your multiple alignment download
> (http://hgdownload.cse.ucsc.edu/goldenPath/dm3/multiz15way/ ) or just
> the Drosophila species (without A. gambiae, A. mellifera and T.
> castaneum)?
>
> And in this case what is the phelogenetic tree used?
>
> Thanks and Regards,
> Richard
>
> On Mon, 2008-11-10 at 13:34 -0800, Brooke Rhead wrote:
>
>> Hello Richard,
>>
>> The EvoFold track uses the information in the "Conservation" and "Most
>> Conserved" tracks (in the Comparative Genomics track group).
>>
>> Note that the EvoFold track on dm3 (D. melanogaster, Apr. 2006) consists
>> of items converted via liftOver from the dm2 assembly (D. melanogaster,
>> Apr. 2004). Therefore, both dm2 and dm3 Evofold tracks use the dm3
>> "Conservation" and "Most Conserved" tracks.
>>
>> You can get to detailed information on both tracks by clicking on the
>> blue track name on the main Genome Browser page
>> (http://genome.ucsc.edu/cgi-bin/hgTracks). The Conservation track
>> details include a list of assemblies that were used for the Multiz
>> alignment, as well as the phylogenetic tree used to generate the
>> multiple alignment.
>>
>> I hope this answers your question. Please feel free to write back to
>> [email protected] if you have further questions.
>>
>> --
>> Brooke Rhead
>> UCSC Genome Bioinformatics Group
>>
>>
>>
>> On 11/09/08 17:42, Richard Lin Zhou wrote:
>>
>>> Is it possible to provide the parameters that were used to generate the
>>> EvoFold track in the Tables on D. melanogaster? (The Phelogenetic tree
>>> and alignment input etc).
>>>
>>> _______________________________________________
>>> Genome maillist - [email protected]
>>> http://www.soe.ucsc.edu/mailman/listinfo/genome
>>>
>
> _______________________________________________
> Genome maillist - [email protected]
> http://www.soe.ucsc.edu/mailman/listinfo/genome
>
_______________________________________________
Genome maillist - [email protected]
http://www.soe.ucsc.edu/mailman/listinfo/genome
