Mouse protein reference database software

Ncbi reference sequence database a comprehensive, integrated, nonredundant, wellannotated set of reference sequences including genomic, transcript, and protein. The mips mammalian protein protein interaction database is a collection of manually curated highquality ppi data collected from the scientific literature by expert curators. It is designed as a database to collect and integrate raw expression data from a wide range of sources, such as rna in situ hybridization, immunohistochemistry, western blots, northern blots and rtpcr. Biogrid database of protein, chemical, and genetic interactions. Proteinprotein interaction networks functional enrichment analysis. The reference proteome of mus musculus is derived from the genome sequence. The mouse gene expression database developed by mouse genome informatics mgi is a community resource for gene expression information from the laboratory mouse.

In particular, the reference sequence refseq database provides. Batch search with uniprot ids or convert them to another type of database id or vice. Open source protein interaction database at the european institute of bioinformatics ebi. We took great care to include only data from individually performed experiments since they usually provide the most reliable evidence for physical interactions. Creating a reference package with cellranger mkref software. Mgi is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease. Gxd has developed an rnaseq and microarray experiment search to quickly and reliably find specific mouse expression studies in arrayexpress and geo. All, gene name, protein class, uniprot keyword, chromosome, external id, reliability score tissue ihc, reliability score mouse brain, reliability score cells. A comprehensive, integrated, nonredundant, wellannotated set of reference sequences including genomic, transcript, and protein. Cell ranger provides prebuilt human and mouse reference packages for use with. Its primary emphasis is on endogenous gene expression during mouse development.

Biogrid is an online interaction respository with data compiled through comprehensive curation efforts. The hprd is a result of an international collaborative effort between the. Mouse genome annotation by the refseq project springerlink. The human protein reference database hprd is a protein database accessible through the internet. Molecular interaction database at university of rome, based on the intact data model and which focuses on experimentally verified protein interactions extracted by database curators from the literature. First, a large body of data on proteinprotein interactions exists in humans, and yet, none of the databases covers this adequately. Align two or more protein sequences using the clustal omega program. If you would like to use your own genome fasta or gene gtf annotations, cell.

Mgimouse genome informaticsthe international database. A comprehensive, integrated, nonredundant, well annotated set of reference sequences including genomic, transcript, and protein. The mips mammalian proteinprotein interaction database is a collection of manually curated highquality. Steps to create prebuilt human hg19, grch38, mouse mm10. Blast basic local alignment search tool blast standalone blast link blink conserved domain search service cd search genome protmap.