Frequently Asked Questions

If you have any other queries, please write to: lpryszcz [at] crg [dot] es.

MetaPhOrs allows multiple query formats: UniProt, Ensembl, RefSeq etc... However, full cross reference is available only for UniProt and Ensembl. If your query wasn't recognised correctly, please try searching by sequence similarity (BLAST SEARCH option).

Try the BLAST search against all species. If there is still no hit, check if your species is available in our database

Go to the genome-wide prediction section, select your species of interest and launch the search. Note that the search can take several seconds or minutes depending on the size of the proteomes.

Orthology/paralogy assignment is based on Consistency score only. If you set a CS cutoff of 0.0, the server will return all homology predictions for your query.

The Consistency score cut-off works exactly the same as for an orthology search: the higher the CS, the more consistent the predictions retrieved, i.e. 1.0 will return only fully consistent paralogy predictions.

Just follow the protein ID link which points to the source database.

Follow the link under tree number. All trees can be explored from the linked page.

MetaPhOrs resources can be directly linked to from your website by using the examples below.

  • Link to orthology predictions for P32375 using default CS cut-off (0.5) and Evidence level (1) - http://orthology.phylomedb.org/?q=single&metaid=P32375
  • Link to the sequence information page of Phy0010CMS - http://orthology.phylomedb.org/?q=seqInfo&seqid=Phy0010CMS

Some of the trees used for calculation of the predictions are not publicly available yet (this only concerns PhylomeDB resources). Therefore, these trees cannot be visualised through the web server.
At the moment, only trees from phylomes: 1, 3, 4, 5, 7, 16, 18, 19, 20, 21, 23, 26, and 28 are available. The trees from other phylomes will be accessible as soon as they are publicly released.

This section was made using iTOL and requires Adobe Flash Player to be display.

We are keen on extending MetaPhOrs to additional phylogenetic datasets. If you have a specific suggestion of a phylogenetic dataset that is extensive and of sufficient quality, please do not hesitate to contact us and we will consider its implementation.

Alignments and trees reconstructed for external orthologous group repositories are available upon request. Additional information about these datasets and about our phylogenetic pipeline is described in detail here.

 The API access to the database is provided upon personal request.

MetaPhOrs relies entirely on phylogenetic trees from various resources. If a particular species is neither of primary interest in any of these sources nor closely related to a species that is, the fraction of its proteins having annotated orthologs/paralogs is likely to be low. For details look at the Statistics section.

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