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Mouse Genome Informatics (MGI) is a free, online database and bioinformatics resource hosted by The Jackson Laboratory, with funding by the National Human Genome Research Institute (NHGRI), the National Cancer Institute (NCI), and the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD). [1]
The C57BL/6 mouse was the second-ever mammalian species to have its entire genome published. [1] The dark coat makes the mouse strain convenient for creating transgenic mice: it is crossed with a light-furred 129 mouse, and the desirable crosses can be easily identified by their mixed coat colors. [1]
MMHCdb is part of the Mouse Genome Informatics consortium (MGI) and was first released in 1998 as the Mouse Tumor Biology (MTB) database. [4] MMHCdb contains genetic and genomic information about inbred mouse strains, genetically engineered mouse models (GEMMs) and Patient Derived Xenograft (PDX) models of human cancer.
Quality of reference genome sequence: As the CCDS data set is built to represent genomic annotations of human and mouse, the quality problems with the human and mouse reference genome sequences become another challenge. Quality problems occur when the reference genome is misassembled.
Ensembl: provides automatic annotation databases for human, mouse, other vertebrate and eukaryote genomes; Ensembl Genomes: provides genome-scale data for bacteria, protists, fungi, plants and invertebrate metazoa, through a unified set of interactive and programmatic interfaces (using the Ensembl software platform)
The web-based application of BLAT can be accessed from the UCSC Genome Bioinformatics Site. [8] Building the index is a relatively slow procedure. Therefore, each genome assembly used by the web-based BLAT is associated with a BLAT server, in order to have a pre-computed index available for alignments.
The Vertebrate Genome Annotation (VEGA) database was first made public in 2004 by the Wellcome Trust Sanger Institute. It was designed to view manual annotations of human, mouse and zebrafish genomic sequences, and it is the central cache for genome sequencing centers to deposit their annotation of human chromosomes. [6]
The Immunological Genome Project (ImmGen) is a collaborative scientific research project that is currently building a gene-expression database for all characterized immune cells in the mouse. The overarching goal of the project is to computationally reconstruct the gene regulatory network in immune cells