[Genome] Chimpanzee self alignments

[Brian Raney]

Hello JJ,

I posted what we have.  Running the net process on the chains
is not very difficult.  You can discover the procedure in the
perl script we generally use to build chains and nets
(kent/src//hg/utils/automation/doBlastzChainNet.pl)
or in our genome build documentation  files which are
also in the kent source hierarchy
 (kent/src/hg/makeDb/doc/hg18.txt for example).

In general, net'ing the self-chains may be counter productive.
Net's make a lot of sense when comparing two different species,
but not so much when it comes to a single species where
several possibly overlapping rounds of duplication have occurred.

brian

On Dec 11, 2007 7:06 PM, J.J. Emerson <jje at gate.sinica.edu.tw > wrote:

> Dear Brian,
> Thanks so much much for providing access to this resource!  It will turn
> out to be quite useful.  I'm most grateful that you've provided all of the
> blastz search work and subsequent chaining.  I definitely would have balked
> at doing this myself if I was required to come up with sufficient server
> time to do that.
>
> I am further interested in organizing these chains into nets in the same
> way that human self-alignments are organized.  If you also have an internal
> results set with these nets, would it be possible for you to provide access
> to it?  Otherwise, could you make available the pipeline/protocol that you
> use to generate self-nets like you do with human?  I'd be willing to do this
> myself, assuming that the computational time won't be prohibitive.  I'm
> guessing that the most time-consuming part of the process is the blastz
> searching, with subsequent steps being rather fast in comparison.
>
> Thanks a lot for all of your help!
>
> Cheers,
>
> J.J.
>
> PS
> If you just happened to be willing net the chains too, I certainly
> wouldn't complain!  In fact, I'd be rather grateful.  However, I would
> completely understand if you are reluctant further process an internal
> results set that you hadn't planned on supporting in the first place.
>
> On Dec 11, 2007, at 8:27 AM, Brian Raney wrote:
>
> Hey J.J.,
>
> As you've noticed, self-chains are not part of the standard UCSC
> cross-species pipeline, but we have chimp self-chains generated
> for internal use that you're welcome to use with the warning that
> these have not been through the UCSC QA process.  Self chains
> are also hard to tune since there is no one whole genome duplication point
> like
> there is in speciation, so self chains are inevitably going to favor
> certain percent i/d duplications over those that are older ( or more
> recent).
>
> http://genome-test.cse.ucsc.edu/goldenPath/panTro2/vsSelf/
>
> brian
>
> On Dec 4, 2007 12:18 AM, J.J. Emerson <jje at gate.sinica.edu.tw > wrote:
>
> > I notice that the self alignments at UCSC are done only for select
> > genomes which appear to be vertebrate, relatively "high quality" and
> > "important".  I was wondering if the chimpanzee genome could be run
> > through the pipeline in order to collect the self alignments?  I know
> > this is a big undertaking, but considering the attention to primate
> > genomics, especially with regard to duplication, this would seem
> > useful, even if the chimp genome isn't as high quality as the human
> > genome.  It seems as if chimp meets most of these criteria well, its
> > assembly quality notwithstanding.  It would be a really great
> > resource, even with the caveats.  I can think of many people who would
> > find such a resource invaluable.
> >
> > Thanks a lot!
> >
> > Cheers,
> >
> > J.J.
> >
> > PS
> > These are some keywords that might help others using a search engine
> > to find this post and its response:
> > Pan troglodytes, paralogy, synteny, self alignment, duplication,
> > chimp, chimpanzee, duplication, CNV
> > _______________________________________________
> > Genome maillist  -   Genome at soe.ucsc.edu
> > http://www.soe.ucsc.edu/mailman/listinfo/genome
> >
>
>
>