Announcement January 6 2023: FAANGMine v1.3 is now available. We are still in the process of adding new RNAseq and FAANG sequence annotation tracks to the JBrowse browsers.
The FAANG (Functional Annotation of ANimal Genomes) Consortium is "a coordinated international action to accelerate genome to phenome" and aims to generate comprehensive maps of functional elements in genomes of domesticated animals. Data generated by the FAANG Consortium will enhance the use of animal models in the biological and biomedical sciences. It will hasten discoveries in fundamental biology, as well as those that impact human health, animal well-being and agricultural production. In order for the FAANG effort to have substantial impacts on science and society, the data must be accessible to scientists and students of diverse disciplines. Effective use of the FAANG data will require data mining tools that enable easy search and retrieval.
FAANGMine is a project supported by the National Science Foundation to address the need for a high performance data mining resource that enables fine-grained querying and integrating the heterogeneous FAANG data with existing information, such as functions of known genes and research datasets. The specific aims of the project are to 1) develop FAANGMine - a high-performance data mining system that integrates genome assemblies and currently available annotation data for FAANG species, 2) extend FAANGMine by integrating new data generated by the FAANG Consortium, 3) create a FAANGMine user community that consists of students and scientists working on genetics of domesticated animal species. FAANGMine will empower animal researchers, with or without bioinformatics programming skills, to leverage the FAANG data in their research, thereby accelerating discoveries that elucidate the genetic basis of phenotypic variation.
FAANGMine v1.3 (January 2023) is available. See the FAANGMine Release Update page for details. This release includes published FAANG sequence annotation data (e.g. histone marks, open chromatin regions, CTCF binding sites, chromatin states and TADs) with associated metadata for bovine, chicken, goat, horse and pig. See the FAANGMine Data Source page for a complete data list and cited publications. FAANGMine also integrates the reference genomes with a variety of external data sources, including genes (NCBI, Ensembl), proteins (UniProt), protein families and domains (InterPro), orthologs and paralogs (Ensembl Compara, OrthoDB), pathways (KEGG, Reactome), interactions (BioGRID, IntAct), Gene Ontology (UniProt), variants and variant effects (Ensembl Variation and the European Variation Archive), QTL (AnimalQTLdb) and publications (PubMed).
Note for FAANGMine v1.2 users: Your user account was copied to FAANGMine v1.3 at 10am CST January 3 2023. Work done after that time was not copied, but you can transfer it manually. Some of your saved lists may have changed due to updated datasets in FAANGMine v1.3. If you have saved lists in FAANGMine v1.2, the process of upgrading your lists will begin after you first login to v1.3, and may take a few moments. You should view your lists under your MyMine tab to check their status.
Please contact us if you have questions or suggestions for FAANGMine.