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I began working with panTro3 assembly of the UCSC. This assembly corresponds to CGSC Build 2.1.3. See here: https://genome.ucsc.edu/FAQ/FAQreleases.html

Now, I have to cross annotations with ENSEMBL (Indeed, I need to use Biomart tool: http://www.ensembl.org/biomart/martview/2e4aac505f5cf5e0ac255b4a215a056c). But It seems that between Release 64 and 65 they passed directly from Chimp 2.1 to Chimp 2.1.4. I researched some information and found that Chimp 2.1.3 renamed as a Pre! See here: http://pre.ensembl.org/Pan_troglodytes/Info/Index and here http://www.ensembl.info/blog/2011/06/10/new-pre-site-for-chimpanzee/

Is it a way to solve this problem? How may I use Chimp 2.1.3 assembly in Biomart with GrCh37 as reference genome (I was using an archived versions of the Ensembl: http://grch37.ensembl.org/biomart/martview/cbe191dccbe8e5a314cfebeaa8862ca0), but seems not possible to cross between different releases of the ENSEMBL.

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    $\begingroup$ Not that Bioinformatics is off-topic here, but you might get better answers over at Biostars, as they are dedicated to bioinformatics. There are not so many around here. $\endgroup$
    – Chris
    Commented May 26, 2015 at 21:02
  • $\begingroup$ There may be other ways. Please edit your question and explain what you're actually trying to do. What do you mean by "cross annotations"? Do you want to find homologous genes? Syntenic regions? If you tell us what you need, we might be able to help without BioMart. $\endgroup$
    – terdon
    Commented May 26, 2015 at 21:53
  • $\begingroup$ @Chris, is bioinformatics off-topic? Or do you mean programming/software related problems? I couldn't see anything about this in the help pages. $\endgroup$
    – ddiez
    Commented May 27, 2015 at 11:17
  • $\begingroup$ @ddiez That's what I am saying, bioinfiormatics is not off-topic. But still you might get better answer at biostars. Just for complementation. $\endgroup$
    – Chris
    Commented May 27, 2015 at 11:30
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    $\begingroup$ @Chris sorry! I read "note that bioinformatics is off-topic here". My brain decided to complete "Not" to "Note"! $\endgroup$
    – ddiez
    Commented May 27, 2015 at 11:32

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