Amphimedon accessions

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30 Jan, 2018 12:49 PM

I have downloaded the Amphimedon orthologs from Treefram however the accession is not the gene accession for Amphimedon they are in this format 'PACXXX' rather than 'AquXXX'. I cannot convert PAC accessions to AquXXX accessions - any help and tips will be appreciated.

  1. Support Staff 1 Posted by Matthieu Muffat... on 30 Jan, 2018 04:46 PM

    Matthieu Muffato's Avatar

    Dear Emily

    TreeFam 9 included the JGI geneset from October 2010, as found in Ensembl Metazoa version 16. It uses Aqu1.* identifiers for genes and PAC_* identifiers for proteins.
    In 2015, a new version of the annotation was released ( ) with Aqu2.* identifiers for both genes and proteins. This is the version now used in Ensembl Metazoa (although the old version is still available as an optional track). I couldn't see any mapping between the old geneset and the new one on Degnan lab's download page:
    You may want to directly contact the authors of the paper.

    Matthieu Muffato

  2. Matthieu Muffato closed this discussion on 30 Jan, 2018 04:46 PM.

  3. Emily Wong re-opened this discussion on 30 Jan, 2018 09:44 PM

  4. 2 Posted by Emily Wong on 30 Jan, 2018 09:44 PM

    Emily Wong's Avatar

    On 31 Jan 2018, at 02:46, Matthieu Muffato <[email blocked]<mailto:[email blocked]>> wrote:

    Hi Mathieu

    Do you know when a new version of term will be run?



  5. Support Staff 3 Posted by Matthieu Muffat... on 31 Jan, 2018 06:37 PM

    Matthieu Muffato's Avatar

    Hi Emily

    Treefam is in the middle of a reorganization of the phylogenetic analyses of Ensembl and Ensembl Genomes. We have generated a new library of HMMs that are going to be used across all Ensembl sites later this year (see and )
    At the moment we don't know how the website is going to change.

    Kind regards,

  6. Matthieu Muffato closed this discussion on 31 Jan, 2018 06:37 PM.

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