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http://globin.cse.psu.edu/

Data and tools for studying the function of DNA sequences, with an emphasis on those involved in the production of hemoglobin. It includes information about naturally-occurring human hemoglobin mutations and their effects, experimental data related to the regulation of the beta-like globin gene cluster, and software tools for comparing sequences with one another to discover regions that are likely to play significant roles.

Proper citation: Globin Gene Server (RRID:SCR_001480) Copy   

•   Source: SciCrunch Registry

http://www.feedexp.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Database of physiologic data and associated metadata related to feeding behavior for a number of mammalian species, including human. The data contain information on muscle activity, bone and muscle strain, jaw and oropharyngeal apparatus motion, and intra-oral pressure and were generated using several techniques (e.g., electromyography, cineradiography, sonomicrometry). The data are searchable and can be downloaded into csv format.

Proper citation: FEED (RRID:SCR_000637) Copy   

•   Source: SciCrunch Registry

http://amp.pharm.mssm.edu/l2n/upload/register.php

A web-based software system that allows users to upload lists of mammalian genes/proteins onto a server-based program for integrated analysis. The system includes web-based tools to manipulate lists with different set operations, to expand lists using existing mammalian networks of protein-protein interactions, co-expression correlation, or background knowledge co-annotation correlation, as well as to apply gene-list enrichment analyses against many gene-list libraries of prior biological knowledge such as pathways, gene ontology terms, kinase-substrate, microRNA-mRAN, and protein-protein interactions, metabolites, and protein domains. Such analyses can be applied to several lists at once against many prior knowledge libraries of gene-lists associated with specific annotations. The system also contains features that allow users to export networks and share lists with other users of the system.

Proper citation: Lists2Networks (RRID:SCR_006323) Copy   

•   Source: SciCrunch Registry

http://linux1.softberry.com/spldb/SpliceDB.html

Database of canonical and non-canonical mammalian splice sites. The information about verified splice site sequences for canonical and non-canonical sites is presented with the supporting evidence. Weight matrices were built for the major splice groups, which can be incorporated into gene prediction programs.

Proper citation: SpliceDB (RRID:SCR_006262) Copy   

•   Source: SciCrunch Registry

http://woldlab.caltech.edu/rnaseq

Software for Mapping and Quantifying Mammalian Transcriptomes by RNA-Seq. Its functions are to (i) assign reads that map uniquely in the genome to their site of origin and, for reads that match equally well to several sites (''multireads''), assign them to their most likely site(s) of origin; (ii) detect splice-crossing reads and assign them to their gene of origin; (iii) organize reads that cluster together, but do not map to an already known exon, into candidate exons or parts of exons; and (iv) calculate the prevalence of transcripts from each known or newly proposed RNA, based on normalized counts of unique reads, spliced reads and multireads. The new candidate RNA regions produced can be thought of as ESTs, and, like ESTs, some are provisionally appended to existing gene models if they meet several additional criteria. Remaining unassigned candidate transcribed regions (labeled RNAFAR features) can then be used in conjunction with other confirming data to develop new or revised gene models.

Proper citation: ERANGE (RRID:SCR_005240) Copy   

•   Source: SciCrunch Registry

http://biocyc.org/

A collection of Pathway/Genome Databases which describes the genome and metabolic pathways of a single organism. The BioCyc collection of Pathway/Genome Databases (PGDBs) provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms. BioCyc PGDBs are generated by software that predicts the metabolic pathway complements of completely sequenced organisms from their genome sequences. They also include the results of a number of other computational inference procedures applied to these genomes, including predictions of which genes code for missing enzymes in metabolic pathways, and predicted operons. The BioCyc Web site provides a suite of software tools for database searching and visualization, for omics data analysis, and for comparative genomics and comparative pathway questions. The databases within the BioCyc collection are organized into tiers according to the amount of manual review and updating they have received. Tier 1 PGDBs have been created through intensive manual efforts, and receive continuous updating. Tier 2 PGDBs were computationally generated by the PathoLogic program, and have undergone moderate amounts of review and updating. Tier 3 PGDBs were computationally generated by the PathoLogic program, and have undergone no review and updating. There are 967 DBs in Tier 3. The downloadable version of BioCyc that includes the Pathway Tools software provides more speed and power than the BioCyc Web site.

Proper citation: BioCyc (RRID:SCR_002298) 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

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://mpromdb.wistar.upenn.edu/

A curated database that strives to annotate gene promoters identified from ChIP-Seq experiment results. The long term goal of the database is to provide an integrated resource for mammalian gene transcriptional regulation and epigenetics. Users can search based on Enterz gene id/symbol, or by tissue/cell specific activity and filter results based on any combination of tissue/cell specificity, known/novel, CpG/NonCpG, and protein-coding/non-coding gene promoters. It is also integrated with GBrowse genome browser for visualiztion of ChIP-seq profiles and display the annotations.

Proper citation: MPromDb (RRID:SCR_002136) Copy   

•   Source: SciCrunch Registry

https://jeonslab.snu.ac.kr/publication/trip-database-2-0-a-manually-curated-information-hub-for-accessing-trp-channel-interaction-network/

A manually curated database of protein-protein interactions (PPIs) for mammalian transient receptor potential (TRP) channels. The detailed summary of PPI data, fits into 4 categories: screening, validation, characterization, and functional consequence. These categorizations give answers for four basic questions about PPIs: how to identify PPIs (screening); how to confirm PPIs (validation); what are biochemical properties of PPIs (characterization); what are biological meaning of PPIs (functional consequence). Users can find in-depth information specified in the literature on relevant analytical methods, gene constructs, and cell/tissue types. The database has a user-friendly interface with several helpful features, including a search engine, an interaction map, and a function for cross-referencing useful external databases.

Proper citation: TRIP Database (RRID:SCR_002058) Copy   

•   Source: SciCrunch Registry

http://www.ariadnegenomics.com/products/databases/resnet/

Databases that represent sets of pre-compiled information on biological relationships and associations, interactions and facts which have been extracted from the biomedical literature using Ariadne's MedScan technology. ResNet databases store information harvested from the entire PubMed in a formal structure that allows searching, retrieval and updating by Pathway Studio user. ResNet is seamlessly installed when Pathway Studio is installed. There are several available ResNet databases: *ResNet Mammalian Database includes data for Human, Rat, and Mouse *ResNet Plant Database has data on Arabidopsis, Rice and several other plants. Features of ResNet: *All extracted relations have linked access to the original article or abstract *Synonyms and homologs are included to maintain gene identity and to obviate redundancy in search results *Users can update ResNet as often as required using the MedScan technology built into all Ariadne products *Updates are made available by Ariadne every quarter To purchase Pathway Studio software with ResNet database, for information, or to schedule a web demonstration, call our sales department at (240) 453-6272, or (866) 340-5040 (toll free)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: RESNET (RRID:SCR_002121) Copy   

•   Source: SciCrunch Registry

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://wiki.c2b2.columbia.edu/califanolab/index.php/Software/ARACNE

An algorithm, using microarray expression profiles, to scale up to the complexity of regulatory networks in mammalian cells, yet general enough to address a wider range of network deconvolution problems. This method uses an information theoretic approach to eliminate the vast majority of indirect interactions typically inferred by pairwise analysis.

Proper citation: ARACNE (RRID:SCR_002180) 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://www.biorep.it/en

Offer biorepository services to public and private research institutes, to the highest standards of quality and safety with the aim of contributing to the advancement of medical research and scientific discovery. The BioRep Cell Repository establishes, maintains and distributes cell line cultures as well as DNA derived from these cultures. The scientific and business affiliation between BioRep and Coriell allows access to more than a million types of cell vials, stored in liquid nitrogen. Cells that have been stored for nearly 50 years, are still viable and available for research purposes today. Thanks to an exclusive agreement with the Coriell Institute for Medical Research, the oldest and largest biorepository of the world, BioRep is specialized in cell lines preparation, in nucleic acid extraction and long term storage in liquid nitrose (-196 degrees C) and in refrigerators (-80 degrees C) of any kind of biosamples, using procedures and standards developed by the Coriell in over 50 years of activity. BioRep and Coriell together constitute one of the few Global Biorepository able to serve the pharmaceutical industries for world wide clinical trials. BioRep facility is specifically designed to give the utmost efficiency and security by implementing Coriell procedures and standards. The BioRep Tissue Repository provides safe and secure storage of tissue specimens as required for medical research and scientific investigation. All tissues are preserved with the most current preservation techniques and processes. In addition to the storage service, BioRep provides Cell Biology, Molecular Biology, Microbiology services developed in ISO 9001:2008 certified laboratories.

Proper citation: BioRep (RRID:SCR_004907) Copy   

•   Source: SciCrunch Registry

http://www.chickest.udel.edu/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. A chicken EST Web site has been created to provide access to the data, and a set of unique sequences has been deposited with GenBank. This site contains over 40,000 EST sequences from the chicken cDNA libraries in the University of Delaware collection. Users can perform keyword searches, BLAST nucleotide sequences against our database, view clusters of similar or overlapping clones, and order clones. The cDNA and gene sequences of many mammalian cytokines and their receptors are known. However, corresponding information on avian cytokines is limited due to the lack of cross-species activity at the functional level or strong homology at the molecular level. To improve the efficiency of identifying cytokines and novel chicken genes, a directionally cloned cDNA library from T-cell-enriched activated chicken splenocytes was constructed, and the partial sequence of 5251 clones was obtained. Sequence clustering indicates that 2357 (42%) of the clones are present as a single copy, and 2961 are distinct clones, demonstrating the high level of complexity of this library. Comparisons of the sequence data with known DNA sequences in GenBank indicate that approximately 25% of the clones match known chicken genes, 39% have similarity to known genes in other species, and 11% had no match to any sequence in the database. Several previously uncharacterized chicken cytokines and their receptors were present in our library. This collection provides a useful database for cataloging genes expressed in T cells and a valuable resource for future investigations of gene expression in avian immunology. Therefore, the Chick EST database was created.

Proper citation: UD Chick EST Project (RRID:SCR_002236) Copy   

•   Source: SciCrunch Registry