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Category Archives: Comparative Genomics
New gene gain/loss tree view in Ensembl
If you are interested in knowing the evolutionary history of your preferred Ensembl gene, you are in luck. Starting from this release (69) Ensembl has a new gene gain/loss tree view just for this purpose. This view shows the evolutionary … Continue reading
Posted in Comparative Genomics, Ensembl, Features, Release News, Web
Tagged phylogenetic trees
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Underlying trees in the GeneTrees
Starting from this release (65), we provide further details on the internal aspects of the GeneTrees. Our trees are built using a several phylogenetic reconstruction methods, each of them resulting in a different tree. These are combined by TreeBeST to … Continue reading
Posted in Comparative Genomics
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Orthologues (in summary)
We have recently added a new table at the top of the Orthologues view. This table shows the number of species that have a 1:1, 1:many or many:many orthology relationship with the current gene. This table shows that information for … Continue reading
Posted in Comparative Genomics, Help & Tips
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Changing to LASTZ
People following the declarations of intentions for the next release (these are sent to announce@ensembl.org) may have noticed that we are releasing LASTZ pairwise alignments instead of BLASTZ ones. LASTZ is written by Bob Harris from the Penn State University … Continue reading
GERP constrained elements via DAS
It is now possible to get the GERP constrained elements via the DAS protocol. For instance the DAS command to get all the GERP elements on the BRCA2 gene (Human chr 13: 32889611-32973347) is:http://www.ensembl.org/das/Homo_sapiens.GRCh37.constrained_element/features?segment=13:32889611,32973347 By default, you obtain both the … Continue reading
Posted in Comparative Genomics
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Which whole-genome multiple aligner? Pecan!
Comparing and assessing the quality of whole-genome multiple alignments is a difficult task. In the protein world, many mathematical models are available. They are based on synonymous and non-synonymous substitutions and the physicochemical similarities among the aminoacids. None of this … Continue reading
Posted in Comparative Genomics
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Musing about Fish Alignments.
Release 57 saw the release of a 5-way EPO alignment across the telost fish – Zebrafish, Stickleback, Medaka, Tetraodon and Fugu. Just recently I’ve spent some time browsing through them. They are very interesting, with the ancestral duplication in Fish … Continue reading
Posted in Comparative Genomics
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Ensembl, Xfam and HMMs
This week, Albert Vilella and myself participated in the Xfam consortium meeting. The meeting focussed on protein, domains and ncRNA classification, and on the new developments of the HMMER package. Although Ensembl is not part of Xfam, we share many … Continue reading
Posted in Comparative Genomics
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Orthologues on the trees
We have added a little trick for orthology-lovers. Starting from the orthologues page, you can choose to switch to the GeneTree. This will highlight the orthologue of interest, as well as the ancestral node that relates both genes. Another useful … Continue reading
New avian and new fish mutliple alignments
Ensembl 57 includes the turkey genome, the third bird in Ensembl. We are now providing a 3-way avian multiple alignments (chicken, turkey and zebra finch) together with GERP constraint analysis. The image shows amniote and bird constrained elements on the … Continue reading
Posted in Comparative Genomics
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