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http://dgv.tcag.ca/dgv/app/home

Public repository that accepts direct submissions and provides archiving, accessioning and distribution of publicly available genomic structural variants, in all species. Variants are accessioned at the study and sample level, granting stable identifiers that can be used in publications. DGVa data is integrated with other EBI resources, including comprehensive EBI search and Ensembl genome browser. Exchanges data with companion database, dbVar, at National Center for Biotechnology Information.NOTE: since 2019 DGVa doesn't accept submissions. Please send the data for submission to European Variation Archive (EVA).

Proper citation: Database of Genomic Variants Archive (DGVa) (RRID:SCR_004896) Copy   

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http://www.bork.embl.de/j/

The main focus of this Computational Biology group is to predict function and to gain insights into evolution by comparative analysis of complex molecular data. The group currently works on three different scales: * genes and proteins, * protein networks and cellular processes, and * phenotypes and environments. They require both tool development and applications. Some selected projects include comparative gene, genome and metagenome analysis, mapping interactions to proteins and pathways as well as the study of temporal and spatial protein network aspects. All are geared towards the bridging of genotype and phenotype through a better understanding of molecular and cellular processes. The services - resources & tools, developed by Bork Group, are mainly designed and maintained for research & academic purposes. Most of services are published and documented in one or more papers. All our tools can be completely customized and integrated into your existing framework. This service is provided by the company biobyte solutions GmbH. Please visit their tools and services pages for full details and more information. Standard commercial licenses for our tools are also available through biobyte solutions GmbH. The group is partially associated with Max Delbr��ck Center for Molecular Medicine (MDC), Berlin.

Proper citation: EMBL - Bork Group (RRID:SCR_000810) Copy   

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http://linus.nci.nih.gov./BRB-ArrayTools.html

A software package for the visualization and statistical analysis of DNA microarray gene expression data. The tools have been developed from the R statistical system, in C and fortran programs and Java applications. They are integrated into Excel as an add-in.

Proper citation: Biometric Research Branch: ArrayTools (RRID:SCR_000778) Copy   

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http://www.isrec.isb-sib.ch/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. The Computational Cancer Genomics (CCG) group is dedicated to the development of analysis tools and databases relating molecular sequences and biological functions. Sponsors: This group is supported by the Swiss Institute of Bioinformatics (SIB).

Proper citation: Computational Cancer Genomics Group (RRID:SCR_000772) Copy   

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http://www.genet.sickkids.on.ca/cftr/

Collection of mutations in CFTR gene for international cystic fibrosis genetics research community. Provides up to date information about individual mutations in CFTR gene. All known CFTR mutations and sequence variants have been converted to standard nomenclature recommended by Human Genome Variation Society. On line process for submission of new mutations has been added.While they continue to ensure quality of data, they urge international community to give them feedback and suggestions. Clinical information in this database relates only to details of discovery of specific mutations. As part of 2010 upgrade, CFTR1 joined new project called CFTR2 - Clinical and Functional TRanslation of CFTR. Links to CFTR2 for many mutations in CFTR1 will provide up-to-date summaries of genotype-phenotype information from patient registries around the world.

Proper citation: Cystic Fibrosis Mutation Database (RRID:SCR_000685) Copy   

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http://megasoftware.net/

Software integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses. Used for comparative analysis of DNA and protein sequences to infer molecular evolutionary patterns of genes, genomes, and species over time. MEGA version 4 expands on existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. MEGA version 6 enables inference of timetrees, as it implements RelTime method for estimating divergence times for all branching points in phylogeny.

Proper citation: MEGA (RRID:SCR_000667) Copy   

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http://eumorphia.publicwebserver3.har.mrc.ac.uk/

A portal documenting a project for the development of novel approaches in phenotyping, mutagenesis and informatics to improve the characterization of mouse models for understanding human molecular physiology and pathology. EUMORPHIA has developed a new robust primary screening platform for determining the phenotype of mice: EMPReSS - European Mouse Phenotyping Resource for Standardised Screens. The project is also focused on training new young scientists by funding them to work in a variety of laboratories to gain a broader swathe of techniques. The project has also identified the need for more trained mouse pathologists. To address this, they are setting up training courses in pathology and working at a European level to establish more training.

Proper citation: Understanding Human Disease Through Mouse Genetics (RRID:SCR_000785) Copy   

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https://monarchinitiative.org/

Repository of information about model organisms, in vitro models, genes, pathways, gene expression, protein and genetic interactions, orthology, disease, phenotypes, publications, and authors, and ability to navigate multi-scale spatial and temporal phenotypes across in vivo and in vitro model systems in context of genetic and genomic data, using semantics and statistics. Discovery system provides basic and clinical science researchers, informaticists, and medical professionals with integrated interface and set of discovery tools to reveal genetic basis of disease, facilitate hypothesis generation, and identify novel candidate drug targets. Database that indexes authoritative information on experimental models of disease from MGI, RGD and ZFIN.

Proper citation: MONARCH Initiative (RRID:SCR_000824) Copy   

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http://mlemire.freeshell.org/SimM.README

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 6th,2023. Gene dropping simulation software. The program is a gzip'ed tar archive and is designed to run under UNIX/Linux operating system.

Proper citation: SIMM (RRID:SCR_000849) Copy   

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http://wannovar.usc.edu/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Web interface to the ANNOVAR software, a tool to annotate functional consequences of genetic variation from high-throughput sequencing data, to help biologists without bioinformatics skills to easily submit a list of mutations (even whole-genome variants calls) to the web server, select the desired annotation categories, and receive functional annotation back by emails. Given a list of single nucleotide variants (SNVs) and insertions / deletions in VCF or ANNOVAR input format, wANNOVAR annotates their functional effects on genes (such as amino acid changes for non-synonymous SNPs), calculate their predicted functional importance scores (such as SIFT and PolyPhen scores), retrieve allele frequencies in public databases (such as the 1000 Genomes Project and NHLBI-ESP 6500 exomes), and implement a variants reduction protocol to identify a subset of potentially deleterious variants., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: wANNOVAR (RRID:SCR_000565) Copy   

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http://dbserv2.informatik.uni-leipzig.de:8080/onex/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Web-based application that integrates versions of 16 life science ontologies including the Gene Ontology, NCI Thesaurus and selected OBO ontologies with data leading back to 2002 in a common repository to explore ontology changes. It allows to study and apply the evolution of these integrated ontologies on three different levels. It provides global ontology evolution statistics and ontology-specific evolution trends for concepts and relationships and it allows the migration of annotations in case a new ontology version was released

Proper citation: OnEx - Ontology Evolution Explorer (RRID:SCR_000602) Copy   

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http://mbl.org

Collection of high resolution images and databases of brains from many genetically characterized strains of mice with aim to systematically map and characterize genes that modulate architecture of mammalian CNS. Includes detailed information on genomes of many strains of mice. Consists of images from approximately 800 brains and numerical data from just over 8000 mice. You can search MBL by strain, age, sex, body or brain weight. Images of slide collection are available at series of resolutions. Apple's QuickTime Plugin is required to view available MBL Movies.

Proper citation: Mouse Brain Library (RRID:SCR_001112) Copy   

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http://www.bioconductor.org/packages/release/bioc/html/categoryCompare.html

A software package for meta-analysis of high-throughput experiments using feature annotations. It calculates significant annotations (categories) in each of two (or more) feature (i.e. gene) lists, determines the overlap between the annotations, and returns graphical and tabular data about the significant annotations and which combinations of feature lists the annotations were found to be significant. Interactive exploration is facilitated through the use of RCytoscape (heavily suggested).

Proper citation: categoryCompare (RRID:SCR_001223) Copy   

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http://soap.genomics.org.cn/

Software package that provides full solution to next generation sequencing data analysis consisting of an alignment tool (SOAPaligner/soap2), a re-sequencing consensus sequence builder (SOAPsnp), an indel finder ( SOAPindel ), a structural variation scanner ( SOAPsv ), a de novo short reads assembler ( SOAPdenovo ), and a GPU-accelerated alignment tool for aligning short reads with a reference sequence. (SOAP3/GPU)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SOAP (RRID:SCR_000689) Copy   

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https://dgrc.bio.indiana.edu/Home

Serves Drosophila research community by collecting and distributing DNA clones and vectors; collecting and distributing Drosophila cell lines; developing and testing genomics technologies for use in Drosophila and assisting members of the research community in their use.

Proper citation: Drosophila Genomics Resource Center (RRID:SCR_002845) Copy   

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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   

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http://www.cs.cmu.edu/~jernst/stem/

The Short Time-series Expression Miner (STEM) is a Java program for clustering, comparing, and visualizing short time series gene expression data from microarray experiments (~8 time points or fewer). STEM allows researchers to identify significant temporal expression profiles and the genes associated with these profiles and to compare the behavior of these genes across multiple conditions. STEM is fully integrated with the Gene Ontology (GO) database supporting GO category gene enrichment analyses for sets of genes having the same temporal expression pattern. STEM also supports the ability to easily determine and visualize the behavior of genes belonging to a given GO category or user defined gene set, identifying which temporal expression profiles were enriched for these genes. (Note: While STEM is designed primarily to analyze data from short time course experiments it can be used to analyze data from any small set of experiments which can naturally be ordered sequentially including dose response experiments.) Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: Short Time-series Expression Miner (STEM) (RRID:SCR_005016) Copy   

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http://www.ihwg.org/

The IHWG Cell and DNA Bank was established as a shared resource to support the scientific projects of the 13th International Histocompatibility Workshop (IHWS). The Research Cell Bank (RCB), located in Fred Hutchinson Cancer Research Center in Seattle, WA, maintains the IHWG inventory. This comprehensive inventory includes B-Lymphoblastoid Cell Lines (B-LCL) from previous International Workshops, HLA heterozygous and homozygous donors, selected families, and individuals of diverse population groups. The RCB maintains stocks of purified DNA derived from these cell lines, as well as DNA reference panels that provide an extensive array of HLA and HLA-related sequence polymorphisms. The RCB also provides cloned HLA genes and B-LCL transfected with selected HLA genes, which are available on a limited basis.

Proper citation: International Histocompatibility Cell and DNA Bank (RRID:SCR_004871) Copy   

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http://ccr.coriell.org/Sections/Collections/NHGRI/?SsId=11

DNA samples and cell lines from fifteen populations, including the samples used for the International HapMap Project, the HapMap 3 Project and the 1000 Genomes Project (except for the CEPH samples). All of the samples were contributed with consent to broad data release and to their use in many future studies, including for extensive genotyping and sequencing, gene expression and proteomics studies, and all other types of genetic variation research. NHGRI led the contribution of the NIH to the International HapMap Project, which developed a haplotype map of the human genome. This haplotype map, called the HapMap is a publicly available tool that allows researchers to find genes and genetic variations that affect health and disease. The samples from four populations used to develop the HapMap were initially housed in the Human Genetic Cell Repository of the National Institute of General Medical Sciences (NIGMS). Except for the Utah CEPH samples that were in the NIGMS Repository before the initiation of the HapMap Project and remain there, the NHGRI Repository now houses all of the HapMap samples. The NHGRI repository also houses the extended set of HapMap samples, which includes additional samples from the HapMap populations and samples from seven additional populations. All of the samples were collected with extensive community engagement, including discussions with members of the donor communities about the ethical and social implications of human genetic variation research. These samples were studied as part of the HapMap 3 Project. The NHGRI repository also houses the samples for the International 1000 Genomes Project. This Project is lightly sequencing genome-wide 2500 samples from 27 populations. This project aims to provide a detailed map of human genetic variation, including common and rare SNPs and structural variants. This map will allow more precise localization of genomic regions that contribute to health and disease. The 1000 Genomes Project includes many of the samples from the HapMap and extended set of HapMap samples, as well as samples being collected from additional populations. Currently, samples from five additional populations are available; the others will become available during 2011 and 2012. No identifying or phenotypic information is available for the samples. Donors gave broad consent for use of the samples, including for genotyping, sequencing, and cellular phenotype studies. Samples collected from other populations for the study of human genetic variation may be added to the collection in the future. The NHGRI Repository distributes high quality lymphoblastoid cell lines and DNA from the samples to researchers. DNA is provided in plates or panels of 70 to 100 samples or as individual samples. Cell cultures and DNA samples are distributed only to qualified professional persons who are associated with recognized research, medical, educational, or industrial organizations engaged in health-related research or health delivery.

Proper citation: NHGRI Sample Repository for Human Genetic Research (RRID:SCR_004528) Copy   

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http://mgc.nci.nih.gov/

NIH initiative project to provide full-length open reading frame (FL-ORF) clones for human, mouse, and rat genes, cow. MGC cDNA clones were obtained by screening of cDNA libraries, by transcript-specific RT-PCR cloning, and by DNA synthesis of cDNA inserts. All MGC sequences are deposited in GenBank and clones can be purchased from distributors of IMAGE consortium. With conclusion of MGC project in March 2009, GenBank records of MGC sequences will be frozen, without further updates. Since definition of what constitutes full-length coding region for some of genes and transcripts for which they have MGC clones will likely change in future, users planning to order MGC clones will need to monitor for these changes. Users can make use of genome browsers and gene-specific databases, such as the UCSC Genome browser, NCBI's Map Viewer, and Entrez Gene, to view relevant regions of genome (browsers) or gene-related information (Entrez Gene).

Proper citation: Mammalian Gene Collection (RRID:SCR_007024) Copy   

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