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http://rgd.mcw.edu

Database for genetic, genomic, phenotype, and disease data generated from rat research. Centralized database that collects, manages, and distributes data generated from rat genetic and genomic research and makes these data available to scientific community. Curation of mapped positions for quantitative trait loci, known mutations and other phenotypic data is provided. Facilitates investigators research efforts by providing tools to search, mine, and analyze this data. Strain reports include description of strain origin, disease, phenotype, genetics, immunology, behavior with links to related genes, QTLs, sub-strains, and strain sources.

Proper citation: Rat Genome Database (RGD) (RRID:SCR_006444) Copy   

•   Source: SciCrunch Registry

http://www.progenygenetics.com/

Fully customizable, comprehensive genetic pedigree and clinical data management software including a multi-user relational database with an integrated pedigree drawing component to manage genetic and pedigree data in one database. Manage Pedigrees, Individuals, SNPs, STRs, Samples, Plates, Genotypes and exports to multiple analysis platforms. (entry from Genetic Analysis Software) * LIMS software, providing advanced sample tracking and management (including functionality to generate and record barcodes) and configurable workflows for your specific environment. * Full genotype management gives users the ability to track not only family-based studies, but Whole Genome Association studies containing 1000''s of samples with large arrays.

Proper citation: PROGENY (RRID:SCR_006647) Copy   

•   Source: SciCrunch Registry

http://bar.utoronto.ca/welcome.htm

Web-based tools for working with functional genomics and other data, including Gene Expression and Protein Tools, Molecular Markers and Mapping Tools, and Other Genomic Tools. Most are designed with the plant (mainly Arabidopsis) researcher in mind, but a couple of them can be useful to the wider research community, e.g. Mouse eFP Browser or BlastDigester. The associated paper for most tools is available.

Proper citation: BAR (RRID:SCR_006748) Copy   

•   Source: SciCrunch Registry

http://humancyc.org/

The HumanCyc database describes human metabolic pathways and the human genome. By presenting metabolic pathways as an organizing framework for the human genome, HumanCyc provides the user with an extended dimension for functional analysis of Homo sapiens at the genomic level. A computational pathway analysis of the human genome assigned human enzymes to predicted metabolic pathways. Pathway assignments place genes in their larger biological context, and are a necessary step toward quantitative modeling of metabolism. HumanCyc contains the complete genome sequence of Homo sapiens, as presented in Build 31. Data on the human genome from Ensembl, LocusLink and GenBank were carefully merged to create a minimally redundant human gene set to serve as an input to SRI''s PathoLogic software, which generated the database and predicted Homo sapiens metabolic pathways from functional information contained in the genome''s annotation. SRI did not re-annotate the genome, but worked with the gene function assignments in Ensembl, LocusLink, and GenBank. The resulting pathway/genome database (PGDB) includes information on 28,783 genes, their products and the metabolic reactions and pathways they catalyze. Also included are many links to other databases and publications. The Pathway Tools software/database bundle includes HumanCyc and the Pathway Tools software suite and is available under license. This form of HumanCyc is faster and more powerful than the Web version.

Proper citation: HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism (RRID:SCR_007050) Copy   

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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://deconseq.sourceforge.net/

Software tool to automatically detect and efficiently remove sequence contaminations from genomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface. The user can upload FASTA or FASTQ files and select the databases used for contamination screening, including seven human genomes, bacterial genomes, and viral genomes. The user can set the thresholds interactivly and see the results directly using the functionality of the graphical interface. The results can be downloaded in joined or separated files in different formats. The coverage-identity plots provide additional information that can guide the selections of the thresholds using color coded points and connecting lines.

Proper citation: DeconSeq (RRID:SCR_007006) Copy   

•   Source: SciCrunch Registry

http://mga.bionet.nsc.ru/soft/maia-1.0/

Software package of programs for complex segregation analysis in animal pedigrees.

Proper citation: MAIA (RRID:SCR_007153) Copy   

•   Source: SciCrunch Registry

http://www.mogene.com/

Core provides services to its partners in deploying genomic capabilities to bring critical solutions to both agriculture and industrial biotech operations. Core facility also provides assistance to research, biotech/pharma and government facilities. In addition to being an Agilent Certified Service Provider MOgene is also a CLIA certified genomics service facility offering one stop service and solution from Tissue/Cells to Analysis. Core offers RNA/DNA isolation, Microarrays, NextGen sequencing, Real time PCR and bioinformatics services.

Proper citation: MOgene (RRID:SCR_012433) Copy   

•   Source: SciCrunch Registry

http://wwwn.cdc.gov/dls/genetics/rmmaterials/default.aspx

The goal of the Genetic Testing Reference Materials Coordination Program (GeT-RM) is to coordinate a self-sustaining community process to improve the availability of appropriate and characterized reference materials for: Quality control (QC), Proficiency testing (PT), Test development & validation, Research. The purpose of this program is: - To help the genetic testing community obtain appropriate and characterized reference materials - To facilitate and coordinate information exchange between users and providers of QC and reference materials - To coordinate efforts for contribution, development, characterization and distribution of reference materials for genetic testing Get-RM provides information about cell lines, DNA, and other kinds of materials that could be used as reference materials for molecular genetic testing. Some of these materials have been characterized by the GeT-RM program and can be divided into three categories: - Genetic Inherited Disease & Pharmacogenetics This section includes information about cell lines, DNA, and other samples that can be used as reference materials for various inherited diseases (including cystic fibrosis, fragile X, Huntington disease, and Ashkenazi Jewish-related diseases), pharmacogenetic loci, and biochemical genetics. The GeT-RM program has confirmed the genotype of many of the genomic DNA samples through testing in multiple clinical genetic laboratories. - Molecular Oncology This section includes information about commercially available cell lines, DNA, and other kinds of materials that could be used as reference materials for various types of cancers, including leukemia/lymphoma and solid tumors. - Infectious Disease This section includes information about commercially available cell lines, DNA, and other kinds of materials that could be used as reference materials for various infectious disease pathogens including viruses, bacteria, and protozoa.

Proper citation: Center for Disease Control and Prevention: Genetic Testing Reference Materials Coordination Program (RRID:SCR_013029) Copy   

•   Source: SciCrunch Registry

http://sift.bii.a-star.edu.sg/

Data analysis service to predict whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations. (entry from Genetic Analysis Software) Web service is also available.

Proper citation: SIFT (RRID:SCR_012813) Copy   

•   Source: SciCrunch Registry

http://web.bioinformatics.ic.ac.uk/eqtlexplorer/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1,2023. eQTL Explorer was developed as a computational resource to visualize and explore data from combined genome-wide expression and linkage studies is essential for the development of testable hypotheses. This visualization tool stores expression profiles, linkage data and information from external sources in a relational database and enables simultaneous visualization and intuitive interpretation of the combined data via a Java graphical interface. eQTL Explorer also provides a new and powerful tool to interrogate these very large and complex datasets. eQTLexplorer allows users to mine and understand data from a repository of genetical genomics experiments. It will graphically display eQTL information based on a certain number of selection criteria, including: tissue type, p-value, cis/trans, probeset Affymetrix id and PQTL type. Sponsors: This work was funded by the MRC Clinical Sciences Centre and the Wellcome Trust programme for Cardiovascular Functional Genomics.

Proper citation: eQTL Visualization Tool (RRID:SCR_013413) Copy   

•   Source: SciCrunch Registry

http://www.jurgott.org/linkage/ListSoftware.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. Listing of computer software for the gene mapping community on the following topics: genetic linkage analysis for human pedigree data, QTL analysis for animal/plant breeding data, genetic marker ordering, genetic association analysis, haplotype construction, pedigree drawing, and population genetics. The inclusion of a program should not be interpreted as an endorsement to that program from us. In the last few years, new technology produces new types of genetic data, and the scope of genetic analyses change dramatically. It is no longer obvious whether a program should be included or excluded from this list. Topics such as next-generation-sequencing (NGS), gene expression, genomics annotation, etc. can all be relevant to a genetic study, yet be specialized topics by themselves. Though programs on variance calling from NSG can be in, those can sequence alignment might be out; programs on eQTL can be in, those on differential expression might be out. This page was created by Dr. Wentian Li, when he was at Columbia University (1995-1996). It was later moved to Rockefeller University (1996-2002), and now takes its new home at North Shore LIJ Research Institute (2002-now). The present copy is maintained by Jurg Ott as a single file. More than 240 programs have been listed by December 2004, more than 350 programs by August 2005, close to 400 programs by December 2006, and close to 480 programs by November 2008, and over 600 programs by October 2012. A version of the searchable database was developed by Zhiliang Hu of Iowa State University, and a recent round of updating was assisted by Wei JIANG of Harbin Medical School. Some earlier software can be downloaded from EBI: ftp://ftp.ebi.ac.uk/pub/software/linkage_and_mapping/ (Linkage and Mapping Software Repository), and http://genamics.com/software/index.htm may contain archived copy of some programs.

Proper citation: Genetic Analysis Software (RRID:SCR_013155) Copy   

•   Source: SciCrunch Registry

http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software application that simultaneously estimates a trait-locus position and its genetic effects for affected relative pairs (ARP) by one of two methods. Either allow a different trait-locus effect for each ARP type, or constrain the trait-locus effects according to the marginal effect of a single susceptibility locus. We include a goodness of fit statistic for the constrained model. (entry from Genetic Analysis Software)

Proper citation: ARP.GEE (RRID:SCR_013134) Copy   

•   Source: SciCrunch Registry

https://doi.org/10.1016/j.genrep.2019.100414

Eutherian comparative genomic analysis protocol as one framework of eutherian gene data set revisions. Protocol integrated gene annotations, phylogenetic analysis and protein molecular evolution analysis with 3 new tests including test of reliability of public eutherian genomic sequences using genomic sequence redundancies, test of contiguity of public eutherian genomic sequences using multiple pairwise genomic sequence alignments and test of protein molecular evolution using relative synonymous codon usage statistics. Public eutherian reference genomic sequence data sets.

Proper citation: Eutherian comparative genomic analysis protocol (RRID:SCR_014401) Copy   

•   Source: SciCrunch Registry

http://www.cisreg.ca/cgi-bin/NHR-scan/nhr_scan.cgi

Web interface for computational prediction of nuclear hormone receptor binding sites in genomic sequences. Flexible Hidden Markov Model framework to allow for variable spacing and orientation of half sites. Allows for parameter modifications.

Proper citation: Nuclear Hormone Receptor Scan (RRID:SCR_016975) Copy   

•   Source: SciCrunch Registry

https://www.iigm.it/site/index.php?l=ENG

Private research institute in Turin, Italy. Research programs in immunogenetics, functional genomics, genomic epidemiology, tumour diagnostic and prognostic biomarker research, epigenetic modifications in disease, quantitative biology and computational neuroscience.

Proper citation: Italian Institute for Genomic Medicine; Turin; Italy (RRID:SCR_017062) Copy   

•   Source: SciCrunch Registry

https://www.a-star.edu.sg/gis/Our-Science/Technology-Platforms/Scientific-and-Research-Computing

Core provides research computing resources including bioinformatics, application development, data management and IT infrastructure to support next generation sequencing technologies, human genotyping, high throughput screening and computational biology researchers.

Proper citation: Genome Institute of Singapore Scientific and Research Computing Core Facility (RRID:SCR_017193) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/GenomicRanges/

Software R package for computing and annotating genomic ranges. Used for storing and manipulating genomic intervals and variables defined along genome.

Proper citation: Genomic Ranges (RRID:SCR_017051) Copy   

•   Source: SciCrunch Registry

https://ircm.qc.ca/en/technological-services/bioinformatics

Core to support scientists within and outside IRCM in analysis of biological and clinical data, in particular high throughput genomic data. Operating on collaborative basis and paid services. Provides assistance with Data analysis for RNA-Seq, ChIP-Seq, RIP-Seq, DNA methylation, DNA-Seq, targeted sequencing of rRNAs, microarrays, customized training courses.

Proper citation: Montreal Clinical Research Bioinformatics Core Facility (RRID:SCR_017176) Copy   

•   Source: SciCrunch Registry

https://arxiv.org/abs/1308.2012

Software tool for estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects. Used as general and assembly independent method for estimating genomic characteristics.

Proper citation: GCE (RRID:SCR_017332) Copy   

•   Source: SciCrunch Registry