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http://www.genomesize.com

Comprehensive catalogue of animal genome size data. Haploid DNA contents (C-values, in picograms) are available for 4972 species (3231 vertebrates and 1741 non-vertebrates) based on 6518 records from 669 published sources. Data may be submitted directly to the database or reprints and notifications of new papers may be sent to database curation staff.

Proper citation: Animal Genome Size Database (RRID:SCR_007551) Copy   

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http://claire.bardel.free.fr/software.html

Software package to perform phylogeny based association and localization analysis.Used for association detection and localization of susceptibility sites using haplotype phylogenetic trees. Performs these two phylogeny-based analysis: tests association between candidate gene and disease; pinpoints markers (SNPs) that are putative disease susceptibility loci.

Proper citation: ALTree (RRID:SCR_007562) Copy   

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http://genes2mind.org

genes2mind is a tool for rapid exploratory analysis of psychotropic drug-induced gene expression in the brain. We present here an open resource containing comparison of effects of various classes of psychotropic drugs on transcriptional alterations of ~20,000 genes in the mouse brain (C57BL/6J). Data stored in the database include raw gene expression values as well as results of drug comparison. * Genomic Signature Identification section allows for the identification of drug-specific genomic signatures. * Genomic Signature Analysis section allows for further inspection and visualization of the signatures using multidimensional data analysis (PCA), co-expression analysis and heatmaps. * Single Gene Inspection allows for brief review of expression of specific candidate genes using barplots.

Proper citation: genes2mind (RRID:SCR_008872) Copy   

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http://www.allelix.net

THIS RESOURCE IS NO LONGER IN SERVICE, documented on September 23, 2013. Software application / data analysis service where one can enter the alleles of commonly used STR by clicking the mouse. The algorithm calculates the paternity index and the Essen-Moeller probability of kinship for the deficiency- and the trio case. Everybody can use the network-software online after registering. The usage on the internet is free. Academic users can ask me to unlock an option to display the details (formulas/frequencies etc.) and to have an export-funktion to MS Word. The program is in German and (non-professional) English. An expansion to other languages is easy, if somebody helps us with the translation. For those who are interested to have the software running on their own intranet (for database security reasons) an individual agreement can be found. (entry from Genetic Analysis Software) (German version is: http://www.allelix.de)

Proper citation: ALLELIX (RRID:SCR_009115) Copy   

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http://wpicr.wpic.pitt.edu/WPICCompGen/bars.htm

Software application that is a statistical method that bridges the gap between single-locus and haplotype-based tests of association. It is based on the non-parametric regression techniques embodied by Bayesian Adaptive Regression Splines. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: BARS (RRID:SCR_009123) Copy   

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https://gmod.org/wiki/CMap.1

Web-based tool that allows users to view comparisons of genetic and physical maps. The package also includes tools for curating map data. (entry from Genetic Analysis Software)

Proper citation: CMAP (RRID:SCR_009034) Copy   

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https://wiki.nci.nih.gov/display/caGWAS/caGWAS

Too that allows researchers to integrate, query, report, and analyze significant associations between genetic variations and disease, drug response or other clinical outcomes. SNP array technologies make it possible to genotype hundreds of thousands of single nucleotide polymorphisms (SNPs) simultaneously, enabling whole genome association studies. Within the Clinical Genomic Object Model (CGOM), the caIntegrator team created a domain model for Whole Genome Association Study Analysis. CGOM-caGWAS is a A semantically annotated domain model that captures associations between Study, Study Participant, Disease, SNP Association Analysis, SNP Population Frequency and SNP annotations. caGWAS APIs and web portal provide: * a semantically annotated domain model, database schema with sample data, seasoned middleware, APIs, and web portal for GWAS data; * platform and disease agnostic CGOM-caGWAS model and associated APIs; * the opportunity for developers to customize the look and feel of their GWAS portal; * a foundation of open source technologies; * a well-tested and performance-enhanced platform, as the same software is being used to house the CGEMS data portal; * accelerated analysis of results from various biomedical studies; and * a single application through which researchers and bioinformaticians can access and analyze clinical and experimental data from a variety of data types, as caGWAS objects are part of the CGOM, which includes microarray, genomic, immunohistochemistry, imaging, and clinical data.

Proper citation: caGWAS (RRID:SCR_009617) Copy   

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http://purl.bioontology.org/ontology/GRO

Ontology that is a conceptual model for the domain of gene regulation. It covers processes that are linked to the regulation of gene expression as well as physical entities that are involved in these processes (such as genes and transcription factors) in terms of ontology classes and semantic relations between classes. GRO is intended to represent common knowledge about gene regulation in a formal way rather than representing extremely fine-grained classes as can be found in ontologies such as the Gene Ontology (GO) (created for data base annotation purposes) and various relevant databases. The main purpose of the ontology is to support NLP applications. It has a particular focus on the relations between processes and the molecules (participants) involved. The basic structure of the GRO is a direct acyclic graph (DAG) with ontology classes as nodes and is-a relations between classes as edges. The taxonomic backbone is further enriched by several semantic relation types (part-of, from-species, participates-in with the two sub-relations agent-of and patient-of).

Proper citation: Gene Regulation Ontology (RRID:SCR_010590) Copy   

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http://www.crg.eu

International biomedical research institute created in December 2000 to discover and advance knowledge for benefit of society, public health and economic prosperity. Non profit foundation. Group leaders are recruited internationally and receive support from centre to set up and run their groups. External Scientific Advisory Board, made up of 15 world leaders in different areas, evaluates them.

Proper citation: Centre for Genomic Regulation; Barcelona; Spain (RRID:SCR_011147) Copy   

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http://www.humanconnectomeproject.org/

A multi-center project comprising two distinct consortia (Mass. Gen. Hosp. and USC; and Wash. U. and the U. of Minn.) seeking to map white matter fiber pathways in the human brain using leading edge neuroimaging methods, genomics, architectonics, mathematical approaches, informatics, and interactive visualization. The mapping of the complete structural and functional neural connections in vivo within and across individuals provides unparalleled compilation of neural data, an interface to graphically navigate this data and the opportunity to achieve conclusions about the living human brain. The HCP is being developed to employ advanced neuroimaging methods, and to construct an extensive informatics infrastructure to link these data and connectivity models to detailed phenomic and genomic data, building upon existing multidisciplinary and collaborative efforts currently underway. Working with other HCP partners based at Washington University in St. Louis they will provide rich data, essential imaging protocols, and sophisticated connectivity analysis tools for the neuroscience community. This project is working to achieve the following: 1) develop sophisticated tools to process high-angular diffusion (HARDI) and diffusion spectrum imaging (DSI) from normal individuals to provide the foundation for the detailed mapping of the human connectome; 2) optimize advanced high-field imaging technologies and neurocognitive tests to map the human connectome; 3) collect connectomic, behavioral, and genotype data using optimized methods in a representative sample of normal subjects; 4) design and deploy a robust, web-based informatics infrastructure, 5) develop and disseminate data acquisition and analysis, educational, and training outreach materials.

Proper citation: MGH-USC Human Connectome Project (RRID:SCR_003490) Copy   

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http://www.genyo.es/en

Center for excellence research in genomic medicine, focusing on the comprehensive study and understanding of the genetic basis of human diseases in general, placing special emphasis on cancer and its genetic disorders related to inheritance. GENYO was created as a multidisciplinary research space, where different professionals from the healthcare, university and business areas interact, making it possible to generate new systems to diagnose, prevent and treat diseases based on the joint and coordinated application of first-rate knowledge in the different areas of genetics. The center is the benchmark center of the Andalusian Program for Research in Clinical Genetics and Genomic Medicine, a program which, together with those of Cell Therapy and Regenerative Medicine, and Nanomedicine have the main objective of supporting and fostering translational research in Advanced Therapies. The activities performed within these three research programs are developed in coordination with the Andalusian Initiative for Advanced Therapies (IATA), an initiative of the Andalusian Government promoted by the Regional Ministries of Health and Innovation, Science and Enterprise.

Proper citation: Centre for Genomics and Oncological Research (RRID:SCR_003920) Copy   

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http://proteininformationresource.org/

Integrated public bioinformatics resource to support genomic, proteomic and systems biology research and scientific studies. Provides databases and protein sequence analysis tools to scientific community, including Protein Sequence Database which grew out from the Atlas of Protein Sequence and Structure. Conducts research in biomedical text mining and ontology, computational systems biology, and bioinformatics cyberinfrastructure. In 2002 PIR, along with its international partners, EBI (European Bioinformatics Institute) and SIB (Swiss Institute of Bioinformatics), were awarded a grant from NIH to create UniProt, a single worldwide database of protein sequence and function, by unifying the PIR-PSD, Swiss-Prot, and TrEMBL databases. Currently, PIR major activities include: i) UniProt (Universal Protein Resource) development, ii) iProClass protein data integration and ID mapping, iii) PRO protein ontology, and iv) iProLINK protein literature mining and ontology development. The FTP site provides free download for iProClass, PIRSF, and PRO.

Proper citation: Protein Information Resource (RRID:SCR_002837) Copy   

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https://genenames.org

Only worldwide authority that provides standardized nomenclature, i.e. gene names and symbols (short form abbreviations), for all known human genes, and stores all approved symbols in the HGNC database. Approved human gene nomenclature. Database of gene symbols and names. Manually curated genes into groups based on shared characteristics such as homology, function or phenotype. Data for protein-coding genes, pseudogenes and non-coding RNAs.

Proper citation: HGNC (RRID:SCR_002827) Copy   

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http://www.broadinstitute.org/scientific-community/science/programs/medical-and-population-genetics/haploview/haploview

A Java based software tool designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses. Haploview currently allows users to examine block structures, generate haplotypes in these blocks, run association tests, and save the data in a number of formats. All functionalities are highly customizable. (entry from Genetic Analysis Software) * LD & haplotype block analysis * haplotype population frequency estimation * single SNP and haplotype association tests * permutation testing for association significance * implementation of Paul de Bakker's Tagger tag SNP selection algorithm. * automatic download of phased genotype data from HapMap * visualization and plotting of PLINK whole genome association results including advanced filtering options Haploview is fully compatible with data dumps from the HapMap project and the Perlegen Genotype Browser. It can analyze thousands of SNPs (tens of thousands in command line mode) in thousands of individuals. Note: Haploview is currently on a development and support freeze. The team is currently looking at a variety of options in order to provide support for the software. Haploview is an open source project hosted by SourceForge. The source can be downloaded at the SourceForge project site.

Proper citation: Haploview (RRID:SCR_003076) Copy   

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http://jaspar.genereg.net

Open source database of curated, non-redundant set of profiles derived from published collections of experimentally defined transcription factor binding sites for multicellular eukaryotes. Consists of open data access, non-redundancy and quality. JASPAR CORE is smaller set that is non-redundant and curated. Collection of transcription factor DNA-binding preferences, modeled as matrices. These can be converted into Position Weight Matrices (PWMs or PSSMs), used for scanning genomic sequences. Web interface for browsing, searching and subset selection, online sequence analysis utility and suite of programming tools for genome-wide and comparative genomic analysis of regulatory regions. New functions include clustering of matrix models by similarity, generation of random matrices by sampling from selected sets of existing models and a language-independent Web Service applications programming interface for matrix retrieval.

Proper citation: JASPAR (RRID:SCR_003030) Copy   

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http://r3cseq.genereg.net/Site/index.html

An R/Bioconductor package to identify chromosomal interaction regions generated by chromosome conformation capture (3C) coupled to next-generation sequencing (NGS), a technique termed 3C-seq. It performs data analysis for a number of different experimental designs, as it can analyze 3C-seq data with or without a control experiment and it can be used to facilitate data analysis for experiments with multiple replicates. The r3Cseq package provides functions to perform data normalization, statistical analysis for cis/trans interactions and visualization in order to help scientists identify genomic regions that physically interact with the given viewpoints of interest. This tool greatly facilitates hypothesis generation and the interpretation of experimental results.

Proper citation: r3Cseq (RRID:SCR_003198) Copy   

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http://www.qgene.org/

A free, open-source, computationally efficient Java program for comparative analyses of QTL mapping data and population simulation that runs on any computer operating system. (entry from Genetic Analysis Software) It is written with a plug-in architecture for ready extensibility. The software accommodates line-cross mating designs consisting of any arbitrary sequence of selfing, backcrossing, intercrossing and haploid-doubling steps that includes map, population, and trait simulators; and is scriptable. Source code is available on request.

Proper citation: QGene (RRID:SCR_003209) Copy   

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http://sagebase.org/

Non-profit biomedical research organization developing predictors of disease and accelerating health research through creation of open systems, incentives, and standards. Formed to coordinate and link academic and commercial biomedical researchers through Commons that represents new paradigm for genomics intellectual property, researcher cooperation, and contributor evolved resources.

Proper citation: Sage Bionetworks (RRID:SCR_003384) Copy   

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http://www.broadinstitute.org/mpg/snap/

A computer program and web-based service for the rapid retrieval of linkage disequilibrium proxy single nucleotide polymorphism (SNP) results given input of one or more query SNPs and based on empirical observations from the International HapMap Project and the 1000 Genomes Project. A series of filters allow users to optionally retrieve results that are limited to specific combinations of genotyping platforms, above specified pairwise r2 thresholds, or up to a maximum distance between query and proxy SNPs. SNAP can also generate linkage disequilibrium plots

Proper citation: SNAP - SNP Annotation and Proxy Search (RRID:SCR_002127) Copy   

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http://rgp.dna.affrc.go.jp/E/index.html

Rice Genome Research Program (RGP) is an integral part of the Japanese Ministry of Agriculture, Forestry and Fisheries (MAFF) Genome Research Project. RGP now aims to completely sequence the entire rice genome and subsequently to pursue integrated goals in functional genomics, genome informatics and applied genomics. It is jointly coordinated by the National Institute of Agrobiological Sciences (NIAS), a government research institute under MAFF and the Society for Techno-innovation of Agriculture, Forestry and Fisheries (STAFF), a semi-private research organization managed and supported by MAFF and a consortium of some twenty Japanese companies. The research is funded with yearly grants from MAFF and additional funds from the Japan Racing Association (JRA). It is now the leading member of the International Rice Genome Sequencing Project (IRGSP), a consortium of ten countries sharing the sequencing of the 12 rice chromosomes. The IRGSP adopts the clone-by-clone shotgun sequencing strategy so that each sequenced clone can be associated with a specific position on the genetic map and adheres to the policy of immediate release of the sequence data to the public domain. In December 2004, the IRGSP completed the sequencing of the rice genome. The high-quality and map-based sequence of the entire genome is now available in public databases.

Proper citation: Rice Genome Research Project (RRID:SCR_002268) Copy   

•   Source: SciCrunch Registry