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http://www.pypop.org/

Open-source software pipeline for population genomics. Designed for processing genotype and allele data and running population genetic analyses, including conformity to Hardy-Weinberg expectations; tests for balancing or directional selection; estimates of haplotype frequencies and measures and tests of significance for linkage disequilibrium.

Proper citation: PyPop (RRID:SCR_013425) Copy   

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http://www.multifactordimensionalityreduction.org/

Software application that is a data mining strategy for detecting and characterizing nonlinear interactions among discrete attributes (e.g. SNPs, smoking, gender, etc.) that are predictive of a discrete outcome (e.g. case-control status). The MDR software combines attribute selection, attribute construction and classification with cross-validation to provide a powerful approach to modeling interactions. (entry from Genetic Analysis Software)

Proper citation: MDR (RRID:SCR_013427) Copy   

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http://lbm.ab.a.u-tokyo.ac.jp/~iwata/antmap/

Software application based on the Ant Colony Optimization to solve the special case of the traveling salesman problem of ordering markers when the number of loci is large. ANYMAP performs segregation test, linkage grouping and locus ordering, and constructs a linkage map rapidly. (entry from Genetic Analysis Software)

Proper citation: ANTMAP (RRID:SCR_013426) Copy   

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http://www.gridqtl.org.uk/

Publicly available Web-based application that can perform QTL mapping on a variety of population types. GridQTL will extend the functionality of QTLExpress by adding new and advanced approaches for modelling QTL analysis in simple and complex populations. These new methods will be available on a Grid system that will offer flexible workflow management, resource allocation, data persistence, detached execution of simulations and the scalability required for the increase in data volume, data sources and complexity required by the new models. (entry from Genetic Analysis Software)

Proper citation: GRIDQTL (RRID:SCR_013397) Copy   

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http://www.tcd.ie/IMM/trinity-biobank/index.php

The Trinity Biobank was established in 2005 to serve the needs of researchers in the area of genetic epidemiology, population genetics and pharmacogenomics. Its services are available to researchers not only in Trinity College but to other institutions at home and abroad. We provide an automated DNA extraction service purifying large volumes blood (up to 10mL whole blood) and tissue DNA for archival and other purposes. In addition it makes available purified DNA and associated GWAS data from 2000 healthy donors for research use. A key requirement for reliable downstream use of DNA is purity and strand size. The quality of DNA in blood and tissue deteriorates upon storage without purification even at -80 degrees C. We ensure rapid turnaround of biological samples through automated extraction using the Qiagen Autopure system based on optimized ''salting out'' chemistry. The purified DNA sample may then be stored safely at -20 degrees C without deterioration thus freeing up valuable -80 degree C freezer space and the associated capital and maintenance cost as well as security and lab space provision. Automated DNA extraction is particularly suitable for high-throughput sample processing called for in epidemiological studies or simply for clearing sample inventory backlogs. The Trinity Biobank distributes control DNA to researchers as part of its remit to enhance the level of research activity and to synergize molecular medicine research nationally and internationally. The buffy coat collection has been made possible with the cooperation of the Irish Blood Transfusion Service (IBTS). An important requirement to access the collection is that the use of the samples relates only to ethically-approved research and to specifically-nominated research projects. The DNA collection consists of high quality human genomic DNA. Each of the available 2,000 samples is from a single individual and each sample comes with the age and gender data of the donor. The buffy coat sample is derived from the total white cell compliment (50mL buffy coat) of a blood donation (c 400mL). We will endeavor to fulfill samples number requests based on age and gender as best as possible. This collection has also been genotyped using the Affymetrix Genome-Wide Human SNP Array 6.0, featuring 1.8 million genetic markers, including more than 906,600 single nucleotide polymorphisms (SNPs) and more than 946,000 probes for the detection of copy number variation (CNV). The DNA comes available as a 100ng/uL in 100uL of TE Buffer, ie in 10ug amounts in a separate screw-cap ampoule. The ampoules are shipped in 100-tube boxes (Sarstedt). Corresponding plasma (ACD) is also available on request. Genotype data is supplied in PLINK binary PED files format (http://pngu.mgh.harvard.edu/~purcell/plink/ ).

Proper citation: Trinity Biobank (RRID:SCR_013279) Copy   

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http://vipbg.vcu.edu/vipbg/trimhap//

Software application for linkage disequilibrium mapping based on ancestral founder haplotypes. Method uses haplotype data from general pedigrees. (entry from Genetic Analysis Software)

Proper citation: TRIMHAP (RRID:SCR_013512) Copy   

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http://www.som.soton.ac.uk/research/geneticsdiv/epidemiology/chromscan/

A statistical based program for association mapping of disease genes. It utilises the Malecot model and the linkage disequilibrium (LD) map for the candidate region to analyse the genotypes derive from large sample of matched cases and controls. (entry from Genetic Analysis Software)

Proper citation: CHROMSCAN (RRID:SCR_013131) Copy   

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software application to compute composite measures of linkage disequilibrium, their variances and covariances, and statistical tests, for all pairs of alleles from two loci when linkage phase is unkown. An extension of Weir and Cockerham (1989) to apply to multi-allelic loci. (entry from Genetic Analysis Software)

Proper citation: COMPOSITELD (RRID:SCR_013132) Copy   

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http://faculty.washington.edu/eathomp/Anonftp/PANGAEA/BOREL/

Software application for inference of genealogical relationships from genetic data, including sibship inference.

Proper citation: BOREL (RRID:SCR_013135) Copy   

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software application for statistical methods for disease and genetic marker associations using cases and their parents. These methods include an extension of the transmission/disequilibrium test (TDT) for multiple marker alleles, as well as additional general tests sensitive to associations that depend on dominant or recessive genetic mechanisms. (entry from Genetic Analysis Software)

Proper citation: GASSOC (RRID:SCR_013136) Copy   

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http://www.bio.unc.edu/faculty/vision/lab/mappop/

Software application that selects high resolution mapping subsamples and performs bin mapping (entry from Genetic Analysis Software)

Proper citation: MAPPOP (RRID:SCR_013490) Copy   

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http://dlin.web.unc.edu/software/SNPMStat/

A command-line program for the statistical analysis of SNP-disease association in case-control/cohort/cross-sectional studies with potentially missing genotype data. SNPMStat allows the user to estimate or test SNP effects and SNP-environment interactions by maximizing the (observed-data) likelihood that properly accounts for phase uncertainty, study design and gene-environment dependence. For SNPs without missing data, the program performs the standard association analysis. For typed SNPs with missing data or untyped SNPs, the program performs the maximum-likelihood analysis. (entry from Genetic Analysis Software)

Proper citation: SNPMSTAT (RRID:SCR_013339) Copy   

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http://www.cbil.ece.vt.edu/ResearchOngoingSNP.htm

Software application (entry from Genetic Analysis Software)

Proper citation: MECPM (RRID:SCR_013341) Copy   

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http://www.bios.unc.edu/~lin/software/MAOS/

Software application that implements valid and efficient statistical methods for meta-analysis of genomewide association studies with overlapping subjects. The current release performs logistic regression analysis of individual level data under the additive mode of inheritance. Data from genome-wide association studies are often analyzed jointly for the purposes of combining information from multiple studies of the same disease or comparing results across different disorders. In many instances, the same subjects appear in multiple studies. Failure to account for overlapping subjects can greatly inflate type I error when combining results from multiple studies of the same disease and can drastically reduce power when comparing results across different disorders. (entry from Genetic Analysis Software)

Proper citation: MAOS (RRID:SCR_013351) Copy   

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http://www.sanger.ac.uk/science/tools/alien-hunter

Software for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs). The predictions (embl format) can be automatically loaded into Artemis genome viewer.

Proper citation: Alien-hunter (RRID:SCR_015967) Copy   

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http://rarge.gsc.riken.go.jp/dsmutant/

RIKEN Arabidopsis Transposon mutants is a series of mutant lines which have a Ds transposon in the genome of Arabidopsis thaliana Nssen ecotype (background by Fedoroff and Smith). This web page provides information on the mutants produced in our laboratory. Each mutant line is assigned by stipulated line codes (ex. 13-4480-1). We determined the flanking sequences of Ds insertion for each independent line. Transposon insertion sites of mutants were estimated by a BLASTN homology against the genome sequence database of Arabidopsis thaliana Columbia ecotype. The closest genes (predicted by AGI) to the transposon insertion sites were picked up. The results of the BLASTP homology search against the nr database of NCBI for the closest genes have been collected for keyword searches.

Proper citation: RIKEN Arabidopsis Transposon mutants (RRID:SCR_003230) Copy   

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http://genome.crg.es/GOToolBox/

The GOToolBox web server provides a series of programs allowing the functional investigation of groups of genes, based on the Gene Ontology resource. The web version of the GOToolBox is free for non-commercial users only. Users from commercial companies are allowed to use the site during a reasonable testing period. For a regular use of the web version, a license fee should be paid. We have developed methods and tools based on the Gene Ontology (GO) resource allowing the identification of statistically over- or under-represented terms in a gene dataset; the clustering of functionally related genes within a set; and the retrieval of genes sharing annotations with a query gene. GO annotations can also be constrained to a slim hierarchy or a given level of the ontology. The source codes are available upon request, and distributed under the GPL license. Platform: Online tool

Proper citation: GOToolBox Functional Investigation of Gene Datasets (RRID:SCR_003192) Copy   

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http://genomequebec.mcgill.ca/PReMod

Database that describes more than 100,000 computational predicted transcriptional regulatory modules within the human genome. These modules represent the regulatory potential for 229 transcription factors families and are the first genome-wide / transcription factor-wide collection of predicted regulatory modules for the human genome. The algorithm used involves two steps: (i) Identification and scoring of putative transcription factor binding sites using 481 TRANSFAC 7.2 position weight matrices (PWMs) for vertebrate transcription factors. To this end, each non-coding position of the human genome was evaluated for its similarity to each PWM using a log-likelihood ratio score with a local GC-parameterized third-order Markov background model. Corresponding orthologous positions in mouse and rat genomes were evaluated similarly and a weighted average of the human, mouse, and rat log-likelihood scores at aligned positions (based on a Multiz (Blanchette et al. 2004) genome-wide alignment of these three species) was used to define the matrix score for each genomic position and each PWM. (ii) Detection of clustered putative binding sites. To assign a module score to a given region, the five transcription factors with the highest total scoring hits are identified, and a p-value is assigned to the total score observed of the top 1, 2, 3, 4, or 5 factors. The p-value computation takes into consideration the number of factors involved (1 to 5), their total binding site scores, and the length and GC content of the region under evaluation. Users can retrieve all information for a given region, a given PWM, a given gene and so on. Several options are given for textual output or visualization of the data.

Proper citation: PReMod (RRID:SCR_003403) Copy   

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http://www-bio3d-igbmc.u-strasbg.fr/ICDS/

Database of interrupted coding sequences detected by a similarity-based approach in complete prokaryotic genomes. The definition of each interrupted gene is provided as well as the ICDS genomic localization with the surrounding sequence. To facilitate the experimental characterization of ICDS, optimized primers are proposed for re-sequencing purposes. The database is accessible by BLAST search or by genome. 118 Genomes are available in the database.

Proper citation: Interrupted CoDing Sequence Database (RRID:SCR_002949) Copy   

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http://biomine.cs.helsinki.fi/

Service that integrates cross-references from several biological databases into a graph model with multiple types of edges, such as protein interactions, gene-disease associations and gene ontology annotations. Edges are weighted based on their type, reliability, and informativeness. In particular, it formulates protein interaction prediction and disease gene prioritization tasks as instances of link prediction. The predictions are based on a proximity measure computed on the integrated graph.

Proper citation: Biomine (RRID:SCR_003552) Copy   

•   Source: SciCrunch Registry