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http://www.wpic.pitt.edu/wpiccompgen/GemTools/GemTools.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software tools for modeling genetic ancestry based on the single nucleotide polymorphism (SNP) information. This package of functions helps the user account for genetic ancestry of a large number of individuals using spectral graph theory and projections to break a large problem into smaller pieces and calculate genetic ancestry information efficiently, i.e., a divide and conquer (dac) strategy. It is completely written in R and runs on any platform that supports R.

Proper citation: GemTools (RRID:SCR_001259) Copy   

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http://med.stanford.edu/tanglab/software/saber.html

Software program suitable for genome-scale data which uses a Markov-hidden Markov model (MHMM) to estimate local ancestry. The MHMM makes it possible to identify genomic blocks of a particular ancestry by use of any high-density single-nucleotide-polymorphism panel. One application is to perform admixture mapping without genotyping special ancestry-informative-marker panels.

Proper citation: SABER (RRID:SCR_001257) Copy   

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http://cran.r-project.org/web/packages/gap/

GAP is designed as an integrated package for genetic data analysis of both population and family data. Currently, it contains functions for sample size calculations of both population-based and family-based designs, classic twin models, probability of familial disease aggregation, kinship calculation, some statistics in linkage analysis, and association analysis involving one or more genetic markers including haplotype analysis with or without environmental covariates.

Proper citation: Genetic Analysis Package (RRID:SCR_003006) Copy   

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http://statgenpro.psychiatry.hku.hk/limx/kggseq/

A biological Knowledge-based mining platform for Genomic and Genetic studies using Sequence data. The software platform, constituted of bioinformatics and statistical genetics functions, makes use of valuable biologic resources and knowledge for sequencing-based genetic mapping of variants / genes responsible for human diseases / traits. It facilitates geneticists to fish for the genetic determinants of human diseases / traits in the big sea of DNA sequences. KGGSeq has paid attention to downstream analysis of genetic mapping. The framework was implemented to filter and prioritize genetic variants from whole exome sequencing data.

Proper citation: KGGSeq (RRID:SCR_005311) Copy   

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http://www.nbiadisorders.org/

The NBIA Disorders Association, formerly known as Hallervorden-Spatz Syndrome Association, (HSSA) was originally founded in 1996 by President, Patricia Wood. The goals of the association are to raise funds to support research pertinent to NBIA; to provide emotional support to those afflicted with NBIA and their families; and to raise public awareness of NBIA. The NBIA Disorders Association is accepting applications for one-year grants for clinical and translational research studies related to the early detection, diagnosis, or treatment of patients with NBIA. Neurodegeneration with Brain Iron Accumulation (NBIA) is a group of rare, genetic, neurological disorders characterized by the accumulation of iron deposits in the brain and progressive degeneration of the nervous system. It typically first appears in childhood. Presenting signs and symptoms may include difficulty walking, loss of balance, and problems related to speech. Those affected suffer a progressive loss of muscle control, sudden involuntary muscle spasms, and uncontrolled tightening of the muscles. Symptoms may also include disorientation, seizures, and deterioration of intellectual ability. Approximately half of the cases diagnosed have been linked to a mutation of a gene known as PANK2. At the present time, symptoms may be treated but there is no cure. The purpose of the NBIA Disorders Association Research Grant Program is to encourage meritorious research studies designed to improve the diagnosis or treatment of NBIA. The research can be conducted in the United States, countries of the European Union, Canada, Australia, New Zealand, Brazil, Argentina, Chile, South Africa, Japan, or Israel, and in other countries where adequate supervision of grant administration is possible. Grants will be awarded to qualified researchers to initiate pilot studies, the results of which are intended to be used to obtain larger multi-year grant funding. Evaluation of proposals will follow NIH guidelines and include careful consideration of experimental or protocol design, objectivity or relevance of parameters measured, and statistical analysis plan. Proposals that address the following areas will be given priority: * Therapeutics Development: ** Development of pantethine and its derivatives ** Development of other rational therapeutics * Animal & Cellular Models: ** Development of a new rodent disease model by targeted insertion of a ''human disease'' mutation into Pank2 ** Development of induced pluripotent stem cell lines. *** Development of animal and cellular models will be considered for multi-year funding with adequate budget justification. Proposals should detail a research plan and a budget for the initial phase of the work, with the option to contract further work out to a commercial enterprise. * Biomarker Discovery and Assay Development: ** Metabolomics ** Coenzyme A / acyl coenzyme A measurement using accessible (peripheral and central) tissue/fluid * New NBIA gene discovery

Proper citation: NBIA Disorders Association (RRID:SCR_005382) Copy   

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https://www.nimhgenetics.org/

Collaborative venture between the National Institute of Mental Health (NIMH) and several academic institutions. Repository facilitates psychiatric genetic research by providing patient and control samples and phenotypic data for wide-range of mental disorders and Stem Cells.Stores biosamples, genetic, pedigree and clinical data collected in designated NIMH-funded human subject studies. RGR database likewise links to other repositories holding data from same subjects, including dbGAP, GEO and NDAR. Allows to access these data and biospecimens (e.g., lymphoblastoid cell lines, induced pluripotent cell lines, fibroblasts) and further expand genetic and molecular characterization of patient populations with severe mental illness.

Proper citation: NIMH Repository and Genomics Resources (RRID:SCR_006698) Copy   

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https://www.ncbi.nlm.nih.gov/pubmed/17539361

Study of twins and their families provides tool for disentangling genetic and environmental origins of traits. Study collected behavioral and psychopathological information using self-, parent and teacher reports, and focused on contributions of genetic and environmental risk factors to psychological health of young people.

Proper citation: Cardiff Study of all Wales and North West of England Twins (RRID:SCR_017480) Copy   

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http://kb.phenoscape.org/

Knowledgebase that uses ontologies to integrate phenotypic data from genetic studies of zebrafish with evolutionary variable phenotypes from the systematic literature of ostariophysan fishes. Users can explore the data by searching for anatomical terms, taxa, or gene names. The expert system enables the broad scale analysis of phenotypic variation across taxa and the co-analysis of these evolutionarily variable features with the phenotypic mutants of model organisms. The Knowledgebase currently contains 565,158 phenotype statements about 2,527 taxa, sourced from 57 publications, as well as 38,189 phenotype statements about 4,727 genes, retrieved from ZFIN. 2013-01-26.

Proper citation: Phenoscape Knowledgebase (RRID:SCR_002821) Copy   

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http://solgenomics.net/

A clade oriented, community curated database containing genomic, genetic, phenotypic and taxonomic information for plant genomes. Genomic information is presented in a comparative format and tied to important plant model species such as Arabidopsis. SGN provides tools such as: BLAST searches, the SolCyc biochemical pathways database, a CAPS experiment designer, an intron detection tool, an advanced Alignment Analyzer, and a browser for phylogenetic trees. The SGN code and database are developed as an open source project, and is based on database schemas developed by the GMOD project and SGN-specific extensions.

Proper citation: SGN (RRID:SCR_004933) Copy   

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http://magest.hgc.jp/

A database for maternal gene expression information for ascidia, colloquially known as sea squirts. Information available includes DNA sequences, expression patterns of ESTs, and cDNA data from uncleaved fertilized eggs. The goal is to utilize the database to understand molecular mechanisms of establishment of embryonic body plans of chordates and to understand evolution from invertebrates to vertebrates in the future.

Proper citation: MAboya Gene Expression Patterns and Sequence Tags (RRID:SCR_000763) Copy   

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http://www.angis.org.au/Databases/Heart/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The aim of this locus-specific mutation database was to provide an online resource that contains summarized and updated information on familial hypertrophic cardiomyopathy (FHC)-associated mutations and related data, for researchers and clinicians. It also serves as a means of publishing previously unpublished data, which could be of value in understanding genotype/phenotype correlations. This database contains mutations in various genes known to cause familial hypertrophic cardiomyopathy, a genetic disorder associated with defects in the sarcomere [1]. Only gene symbols approved by HUGO are used and mutations are reported in accordance with guidelines recommended by the Mutation Database Initiative of HUGO and EBI.

Proper citation: Familial Hypertrophic Cardiomyopathy DNA Mutation Database (RRID:SCR_002346) Copy   

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http://dirline.nlm.nih.gov/

THIS RESOURCE IS NO LONGER IN SERVICE, documented July 15, 2016. Database containing location and descriptive information about a wide variety of information resources including organizations, research resources, projects, and databases concerned with health and biomedicine. This information may not be readily available in bibliographic databases. Each record may contain information on the publications, holdings, and services provided. These information resources fall into many categories including federal, state, and local government agencies; information and referral centers; professional societies; self-help groups and voluntary associations; academic and research institutions and their programs; information systems and research facilities. Topics include HIV/AIDS, maternal and child health, most diseases and conditions including genetic and other rare diseases, health services research and technology assessment. DIRLINE can be searched using subject words (such as disease or condition) including Medical Subject Headings (MeSH) or for the name or location of a resource. It now offers an A to Z list of over 8,500 organizations.

Proper citation: Directory of Health Organizations Online (RRID:SCR_002331) Copy   

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http://www.dogmap.ch/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. An international collaboration between 46 labs from 20 different countries towards a low resolution canine marker map under the auspices of the International Society for Animal Genetics (ISAG). The map under development should achieve a resolution of about 20 cM and some of the markers should be mapped physically. The participants have agreed to use microsatellites as markers on a common panel of reference families which will provide the backbone of the marker map. It is foreseen to also include type I markers in the mapping effort and to produce cosmid derived microsatellites for physical mapping. For this purpose part of the effort focuses on the standardization of the canine karyotype. Special attention is payed to hereditary diseases where efforts are under way to establish resource families either by collecting families or by specific breeding. A point of emphasis of the DogMap project is the setting up of an internationally accessible database for handling the mapping data. The structure of the DogMap collaboration includes a managing committee and scientific advisers. The managing committee is responsible for the overall coordination of the activities within the collaboration, for the dissemination of relevant information to all of the participants and for the representation of DogMap outside the collaboration., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: DogMap (RRID:SCR_002332) Copy   

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http://www.ala.org.au/

Online repository of information about Australian plants, animals, and fungi. Development started in 2006. The Commonwealth Scientific and Industrial Research Organisation is organisation significantly involved in development of ALA.

Proper citation: Atlas of Living Australia (RRID:SCR_006467) Copy   

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http://yh.genomics.org.cn

This database presents the entire DNA sequence of the first diploid genome sequence of a Han Chinese, a representative of Asian population. The genome, named as YH, represents the start of YanHuang Project, which aims to sequence 100 Chinese individuals in 3 years. It was assembled based on 3.3 billion reads (117.7Gbp raw data) generated by Illumina Genome Analyzer. In total of 102.9Gbp nucleotides were mapped onto the NCBI human reference genome (Build 36) by self-developed software SOAP (Short Oligonucleotide Alignment Program), and 3.07 million SNPs were identified. The personal genome data is illustrated in a MapView, which is powered by GBrowse. A new module was developed to browse large-scale short reads alignment. This module enabled users track detailed divergences between consensus and sequencing reads. In total of 53,643 HGMD recorders were used to screen YH SNPs to retrieve phenotype related information, to superficially explain the donor's genome. Blast service to align query sequences against YH genome consensus was also provided.

Proper citation: YanHuang Project (RRID:SCR_006077) Copy   

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http://msub.csbio.unc.edu/

A custom genome browser which provides detailed answers to questions on the haplotype diversity and phylogenetic origin of the genetic variation underlying any genomic region of most laboratory strains of mice (both classical and wild-derived). Users can select a region of the genome and a set of laboratory strains and/or wild caught mice. The region is selected by specifying the start (e.g. 31200000 or 31200K or 31.2M), and end of the interval and the chromosome (i.e, autosome number and X chromosome). Samples can be selected by name or by entire set. Data sets include information on subspecific origin, heterozygosity regions, and haplotype coloring, among others.

Proper citation: Mouse Phylogeny Viewer (RRID:SCR_014071) Copy   

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http://www.cmbi.ru.nl/GeneSeeker/

The GeneSeeker allows you to search across different databases simultaneously, given a known human genetic location and expression/phenotypic pattern. The GeneSeeker returns any found gene names which are located on the specified location and expressed in the specified tissue. To search for more expression location in one search, just enter them in the textbox for the expression location and separate them with logical operators (and, or, not). You can specify as many tissues as you want, the program starts 20 queries simultaneously, and then waits for a query to finish before starting another query, to keep server loads to a minimum. You can also search only for expression, just leave the cytogenetic location fields blank, and do the query. If you only want to look for one cytogenetic location, only fill in the first location field, and the GeneSeeker will search with only this one. Housekeeping genes , found in Swissprot can be excluded, or genes that are to be excluded can be specified. Human chromosome localizations are translated with an oxford-grid to mouse chromosome localizations, and then submitted to the Mgd. Sponsors: GeneSeeker is a service provided by the Centre for Molecular and Biomolecular Informatics (CMBI).

Proper citation: GeneSeeker (RRID:SCR_008347) Copy   

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http://mips.gsf.de/services/genomes/uwe25/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. This is the official database of the environmental chlamydia genome project. This resource provides access to finished sequence for Parachlamydia-related symbiont UWE25 and to a wide range of manual annotations, automatical analyses and derived datasets. Functional classification and description has been manually annotated according to the Annotation guidelines. Chlamydiae are the major cause of preventable blindness and sexually transmitted disease. Genome analysis of a chlamydia-related symbiont of free-living amoebae revealed that it is twice as large as any of the pathogenic chlamydiae and had few signs of recent lateral gene acquisition. We showed that about 700 million years ago the last common ancestor of pathogenic and symbiotic chlamydiae was already adapted to intracellular survival in early eukaryotes and contained many virulence factors found in modern pathogenic chlamydiae, including a type III secretion system. Ancient chlamydiae appear to be the originators of mechanisms for the exploitation of eukaryotic cells. Environmental chlamydiae have recently been recognized as obligate endosymbionts of free-living amoebae and have been implicated as potential human pathogens. Environmental chlamydiae form a deep branching evolutionary lineage within the medically important order Chlamydiales. Despite their high diversity and ubiquitous distribution in clinical and environmental samples only limited information about genetics and ecology of these microorganisms is available. The Parachlamydia-related Acanthamoeba symbiont UWE25 was therefore selected as representative environmental chlamydia strain for whole genome sequencing. Comparative genome analysis was performed using PEDANT and simap. Sponsors: The environmental chlamydia genome project was funded by the bmb+f (German Federal Ministry of Education and Research) and is part of the Competence Network PathoGenoMiK.

Proper citation: Protochlamydia amoebophila UWE25 (RRID:SCR_008222) Copy   

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http://mips.gsf.de/genre/proj/ustilago/

The MIPS Ustilago maydis Genome Database aims to present information on the molecular structure and functional network of the entirely sequenced, filamentous fungus Ustilago maydis. The underlying sequence is the initial release of the high quality draft sequence of the Broad Institute. The goal of the MIPS database is to provide a comprehensive genome database in the Genome Research Environment in parallel with other fungal genomes to enable in depth fungal comparative analysis. The specific aims are to: 1. Generate and assemble Whole Genome Shotgun sequence reads yielding 10X coverage of the U. maydis genome 2. Integrate the genomic sequence assembly with physical maps generated by Bayer CropScience 3. Perform automated annotation of the sequence assembly 4. Align the strain 521 assembly with the FB1 assembly provided by Exelixis 5. Release the sequence assembly and results of our annotation and analysis to public Ustilago maydis is a basidiomycete fungal pathogen of maize and teosinte. The genome size is approximately 20 Mb. The fungus induces tumors on host plants and forms masses of diploid teliospores. These spores germinate and form haploid meiotic products that can be propagated in culture as yeast-like cells. Haploid strains of opposite mating type fuse and form a filamentous, dikaryotic cell type that invades plant tissue to reinitiate infection. Ustilago maydis is an important model system for studying pathogen-host interactions and has been studied for more than 100 years by plant pathologists. Molecular genetic research with U. maydis focuses on recombination, the role of mating in pathogenesis, and signaling pathways that influence virulence. Recently, the fungus has emerged as an excellent experimental model for the molecular genetic analysis of phytopathogenesis, particularly in the characterization of infection-specific morphogenesis in response to signals from host plants. Ustilago maydis also serves as an important model for other basidiomycete plant pathogens that are more difficult to work with in the laboratory, such as the rust and bunt fungi. Genomic sequence of U. maydis will also be valuable for comparative analysis of other fungal genomes, especially with respect to understanding the host range of fungal phytopathogens. The analysis of U. maydis would provide a framework for studying the hundreds of other Ustilago species that attack important crops, such as barley, wheat, sorghum, and sugarcane. Comparisons would also be possible with other basidiomycete fungi, such as the important human pathogen C. neoformans. Commercially, U. maydis is an excellent model for the discovery of antifungal drugs. In addition, maize tumors caused by U. maydis are prized in Hispanic cuisine and there is interest in improving commercial production. The complete putative gene set of the Broad Institute''s second release is loaded into the database and in addition all deviating putative genes from a putative gene set produced by MIPS with different gene prediction parameters are also loaded. The complete dataset will then be analysed, gene predictions will be manually corrected due to combined information derived from different gene prediction algorithms and, more important, protein and EST comparisons. Gene prediction will be restricted to ORFs larger than 50 codons; smaller ORFs will be included only if similarities to other proteins or EST matches confirm their existence or if a coding region was postulated by all prediction programs used. The resulting proteins will be annotated. They will be classified according to the MIPS classification catalogue receiving appropriate descriptions. All proteins with a known, characterized homolog will be automatically assigned to functional categories using the MIPS functional catalog. All extracted proteins are in addition automatically analysed and annotated by the PEDANT suite.

Proper citation: MIPS Ustilago maydis Database (RRID:SCR_007563) Copy   

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http://escience.invitrogen.com/ipath/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. LINNEA Pathways is a user-friendly comprehensive online resource for gene- or protein-based scientific research. It is based on a total of 248 signaling and metabolic human biological pathway maps created for Invitrogen by GeneGo. The current version of iPath features 225 maps displaying human regulatory and metabolic pathways established in experimental literature produced by MetaCore from GeneGo, Inc. The map objects (proteins, genes, EC functions, and compounds) are connected via metabolic transformations and physical protein interactions, which were assembled by the GeneGo team of experienced annotators, geneticists, and biochemists. The pathways are organized in a vertical fashion following the general signaling path from signaling molecules and membrane receptors, via signal transduction cascades, to transcription factors and their gene targets. Following the natural organization of cellular machinery with highly interconnected pathways and modules, many maps are linked together via hyperlinked box symbols. Such linkage allows the reconstruction of a big picture view of human cell biology., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Invitrogen iPath (RRID:SCR_008120) Copy   

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