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http://mips.helmholtz-muenchen.de/genre/proj/corum

Database of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, but data from high-throughput experiments is excluded.
The majority of protein complexes in CORUM originates from man (65%), followed by mouse (14%) and rat (14%)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: CORUM (RRID:SCR_002254) Copy   

•   Source: SciCrunch Registry

http://geneseer.com/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Database to access gene information through common names and allows identification of homologs and paralogs for a given gene. This publicly available tool leverages public sequence data, gene metadata information, and other publicly available data to calculate and display orthologous and paralogous gene relationships for all genes from several species, including yeasts, insects, worms, vertebrates, mammals, and primates such as humans.

Proper citation: GeneSeer (RRID:SCR_002626) Copy   

•   Source: SciCrunch Registry

http://xavante.fmrp.usp.br/mammibase/

Database developed to assist the phylogeneticist user in retrieving individual gene sequence alignments for genes in complete mammalian mitochondrial genomes. Data retrieval in MamMiBase requires three stages. At the first stage, the user must select the mammalian species or group that (s)he wishes to study. In the second stage, the user will select the outgroup from a list that included all species selected in the first stage plus Xenopus laevis and Gallus gallus. Finally, at the third stage, the user will select individual mitochondrial gene alignments or a phylogenetic tree that (s)he wishes to download.

Proper citation: Mammalian Mitochondrial Genomics Database (RRID:SCR_003084) Copy   

•   Source: SciCrunch Registry

http://research.imb.uq.edu.au/rnadb

A comprehensive mammalian noncoding RNA database containing sequences and annotations for tens of thousands of noncoding RNAs. These include a wide range of microRNAs, small nucleolar RNAs and larger mRNA-like ncRNAs. All raw data from the original RNAdb 2.0 database can be downloaded in XML or FASTA format. This website serves to archive the final snapshot of the RNAdb 2.0 datasets for legacy purposes. It will remain active indefinitely.

Proper citation: RNAdb (RRID:SCR_003578) Copy   

•   Source: SciCrunch Registry

http://goblet.molgen.mpg.de/cgi-bin/goblet2008/goblet.cgi

Tool that performs annotation based on GO and pathway terms for anonymous cDNA or protein sequences. It uses the species independent GO structure and vocabulary together with a series of protein databases collected from various sites, to perform a detailed GO annotation by sequence similarity searches. The sensitivity and the reference protein sets can be selected by the user. GOblet runs automatically and is available as a public service on our web server. GOblet expects query sequences to be in FASTA-Format (with header-lines). Protein and nucleotide sequences are accepted. Total size of all sequences submitted per request should not be larger than 50kb currently. For security reasons: Larger post's will be rejected. Due to limited capacities the queries may be processed in batches depending on the server load. The output of the BLAST job is filtered automatically and the relevant hits are displayed. In addition, the respective GO-terms are shown together with the complete GO-hierarchy of parent terms., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GOblet (RRID:SCR_006998) Copy   

•   Source: SciCrunch Registry

http://mampol.uab.es

Database providing a collection of all the existing polymorphic sequences in the Mammalia group. It allows the search for any polymorphic set according to different parameter values of nucleotide diversity. For data collection, diversity measures and updating they use PDA, a pipeline made of a set of Perl modules that automates the process of sequence retrieving, grouping, aligning and estimating diversity parameters from GenBank sequences. Diversity measures, including polymorphism estimates in synonymous and non-synonymous sites, linkage disequilibrium and codon bias, are calculated for each polymorphic set in different functional regions. The database also includes the primary information retrieved from different external sources: the mammalian publicly available nucleotide sequences (excluding ESTs, STSs, GSSs, working draft and patents) with their annotations and references from GenBank, and the cross-references to the PopSet database. The database content is daily updated, and records are assigned unique and permanent MamPol identification numbers to facilitate cross-database referencing.

Proper citation: MamPolMammalia Polymorphism Database (RRID:SCR_007769) Copy   

•   Source: SciCrunch Registry

https://obofoundry.org/ontology/cl.html

Ontology designed as a structured controlled vocabulary for cell types. It was constructed for use by the model organism and other bioinformatics databases. It includes cell types from prokaryotes, mammals, and fungi. The ontology is available in the formats adopted by the Open Biological Ontologies umbrella and is designed to be used in the context of model organism genome and other biological databases.

Proper citation: Cell Type Ontology (RRID:SCR_004251) Copy   

•   Source: SciCrunch Registry

http://www.cbs.dtu.dk/services/NetOGlyc/

Server that produces predictions of mucin-type GalNAc O-glycosylation sites in mammalian proteins.

Proper citation: NetOGlyc (RRID:SCR_009026) Copy   

•   Source: SciCrunch Registry

http://targetscan.org/

Web tool to predict biological targets of miRNAs by searching for presence of conserved 8mer, 7mer and 6mer sites that match seed region of each miRNA. Nonconserved sites are also predicted and sites with mismatches in seed region that are compensated by conserved 3' pairing. Used to search for predicted microRNA targets in mammals.

Proper citation: TargetScan (RRID:SCR_010845) Copy   

•   Source: SciCrunch Registry

http://pcidb.russelllab.org/

The database of protein-chemical structural interactions includes all existing 3D structures of complexes of proteins with low molecular weight ligands. When one considers the proteins and chemical vertices of a graph, all these interactions form a network. Biological networks are powerful tools for predicting undocumented relationships between molecules. The underlying principle is that existing interactions between molecules can be used to predict new interactions. For pairs of proteins sharing a common ligand, we use protein and chemical superimpositions combined with fast structural compatibility screens to predict whether additional compounds bound by one protein would bind the other. The current version includes data from the Protein Data Bank as of August 2011. The database is updated monthly.

Proper citation: ProtChemSI (RRID:SCR_006115) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/mammals/haploreg/haploreg.php

HaploReg is a tool for exploring annotations of the noncoding genome at variants on haplotype blocks, such as candidate regulatory SNPs at disease-associated loci. Using linkage disequilibrium (LD) information from the 1000 Genomes Project, linked SNPs and small indels can be visualized along with their predicted chromatin state in nine cell types, conservation across mammals, and their effect on regulatory motifs. HaploReg is designed for researchers developing mechanistic hypotheses of the impact of non-coding variants on clinical phenotypes and normal variation.

Proper citation: HaploReg (RRID:SCR_006796) Copy   

•   Source: SciCrunch Registry

http://www.scienceexchange.com/facilities/division-of-comparative-pathology-miami

The Division of Comparative Pathology is a full service veterinary pathology laboratory with both clinical pathology and histology services. Routine hematology and serum biochemistry testing is available for multiple species; we work well with low volume samples. Specialized testing is available or can be implemented as needed. Routine histology services including processing, embedding, and sectioning are available with many routine and special staining options.

Proper citation: UM Miller School of Medicine Division of Comparative Pathology (RRID:SCR_012492) Copy   

•   Source: SciCrunch Registry