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MitoMiner Version 4.0 Released!
Fri, 2016-04-29 17:33 — Anthony Smith
We have made a significant changes to MitoMiner to produce version 4.0. The most noticeable change is moving from a UniProt protein centric database to a Ensembl Gene centric database. We have also narrowed the focus of the database to 6 organisms: H. sapiens, M. musculus, R. norvegicus, D. rerio, S. cerevisiae, S. pombe. This has significantly reduced redundant entries and has made the database much easier to navigate and search. We have also included many new data types including phenotypes and interaction data. If you have any questions or comments you can write to us at mitominer@mrc-mbu.cam.ac.uk. The old protein centric version is still available and can be found here: http://mitominer.mrc-mbu.cam.ac.uk/release-3.1-archive/
Enhancements included for Version 4.0:
Zebrafish
We now include annotation and homology data for Zebrafish.
Phenotypes
We include phenotype data from MGI, Zebrafish and S. cerevisiae.
Interaction data
We include protein and genetic interaction data from BioGRID for all the species included in MitoMiner.
Gene Homology
We have now switched from the NCBI's HomoloGene to Ensembl Compara.
Mitochondrial Targeting Sequences
We now include MitoFates predictions (http://mitf.cbrc.jp/MitoFates/cgi-bin/top.cgi) as well as iPSORT, MitoProt and TargetP. We also now include cleavage site predictions from MitoFates and MitoProt.
Integrated Mitochondrial Protein Index (IMPI) - reference set
MitoMiner now includes an updated IMPI dataset of mitochondrial genes that was created using the new data in MitoMiner 4.0. Further details can be found on the IMPI page: http://mitominer.mrc-mbu.cam.ac.uk/release-4.0-beta/impi.do
Many of the other datasources have been refreshed and updated. Further details can be found here: http://mitominer.mrc-mbu.cam.ac.uk/release-4.0-beta/dataCategories.do
Users of Version 3.1
The new version of MitoMiner uses a new database structure. This was unavoidable and unfortunately means that we are unable to transfer user accounts from the previous version. Therefore existing users will have to set up a new account in v4.0. If you have any queries that you have built in the last version that you would like to use in this new version please contact us. We will be happy to convert them to be compatible with the new database structure.