Autarchy of the Private Cave

MultiParanoid

Here we present a new proteome-scale analysis program called MultiParanoid that can automatically find orthology relationships between proteins in multiple proteomes. The software is an extension of the InParanoid program that identifies orthologs and inparalogs in pairwise proteome comparisons. MultiParanoid applies a clustering algorithm to merge multiple pairwise ortholog groups from InParanoid into multi-species ortholog groups.

QuickParanoid

QuickParanoid is a suite of programs for automatic ortholog clustering and analysis. It takes as input a collection of files produced by InParanoid and finds ortholog clusters among multiple species. For a given dataset, QuickParanoid first preprocesses each InParanoid output file and then computes ortholog clusters. It also provides a couple of programs qa1 and qa2 for analyzing the result of ortholog clustering.

So… both use InParanoid… Are there any differences? Let me list those which I’ve found.

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For the COTRASIF tool, I’ve been using the Ensembl Compara database (since release 47) to automatically import into COTRASIF gene orthology mappings.

However, with the E!50 release, the Compara database was dropped.

Looking for another option to get orthologs from Ensembl (using martservice, via biomart.org), I tried using the standard query – selecting “Homologs” group on the “Attributes” page for a single species database, and then selecting appropriate second species to get orthology mappings.

Imagine my surprise, when not only in the interface, but also in the generated XML file I found attribute names like “cow_ensembl_gene” :-O

I only need 11 species at the moment, and excluding the sufficiently unique name mappings like “zebrafish – danio rerio”, there is a number of questionable mappings: “yeast” for S. cerevisiae (could be S.pombe), “rat” for R. norvegicus (could be R.rattus), “anopheles” for A.gambiae (could be some other Anopheles). Other mappings might be also non-unique, especially for people working with different species of the same genus.

Am I missing some system in this naming “convention”, or am I the only one who finds it strange?

Is there a way not to use “common species names” when importing orthology data from Ensembl with the help of martservice?