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.
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Support Staff 1 Posted by Matthieu Muffat... on 30 Jan, 2018 04:46 PM
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 (http://europepmc.org/abstract/MED/25975661 ) 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: http://amphimedon.qcloud.qcif.edu.au/downloads.html
You may want to directly contact the authors of the paper.
Matthieu Muffato closed this discussion on 30 Jan, 2018 04:46 PM.
Emily Wong re-opened this discussion on 30 Jan, 2018 09:44 PM
2 Posted by Emily Wong on 30 Jan, 2018 09:44 PM
On 31 Jan 2018, at 02:46, Matthieu Muffato <[email blocked]<mailto:[email blocked]>> wrote:
Do you know when a new version of term will be run?
Support Staff 3 Posted by Matthieu Muffat... on 31 Jan, 2018 06:37 PM
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 http://www.ensembl.org/info/genome/compara/hmm_lib.html and ftp://ftp.ensembl.org/pub/current_compara/ )
At the moment we don't know how the treefam.org website is going to change.
Matthieu Muffato closed this discussion on 31 Jan, 2018 06:37 PM.