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http://stothard.afns.ualberta.ca/downloads/NGS-SNP/

A collection of command-line scripts for providing rich annotations for SNPs identified by the sequencing of transcripts or whole genomes from organisms with reference sequences in Ensembl. Included among the annotations, several of which are not available from any existing SNP annotation tools, are the results of detailed comparisons with orthologous sequences. These comparisons allow, for example, SNPs to be sorted or filtered based on how drastically the SNP changes the score of a protein alignment. Other fields indicate the names of overlapping protein domains or features, and the conservation of both the SNP site and flanking regions. NCBI, Ensembl, and Uniprot IDs are provided for genes, transcripts, and proteins when applicable, along with Gene Ontology terms, a gene description, phenotypes linked to the gene, and an indication of whether the SNP is novel or known. A ?Model_Annotations? field provides several annotations obtained by transferring in silico the SNP to an orthologous gene, typically in a well-characterized species.

Proper citation: NGS-SNP (RRID:SCR_005182) 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   

•   Source: SciCrunch Registry

http://bioapps.sabanciuniv.edu/mugex/v02/

Service that automatically extracts mutation-gene pairs from MEDLINE abstracts for a given disease.

Proper citation: MuGeX (RRID:SCR_005306) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/netclassr/

An R package for network-based feature (gene) selection for biomarkers discovery via integrating biological information. The package adapts the following 5 algorithms for classifying and predicting gene expression data using prior knowledge: # average gene expression of pathway (aep); # pathway activities classification (PAC); # Hub network classification (hubc); # filter via top ranked genes (FrSVM); # network smoothed t-statistic (stSVM).

Proper citation: netClass (RRID:SCR_005672) Copy   

•   Source: SciCrunch Registry

http://gmod.org/wiki/Flash_GViewer

Flash GViewer is a customizable Flash movie that can be easily inserted into a web page to display each chromosome in a genome along with the locations of individual features on the chromosomes. It is intended to provide an overview of the genomic locations of a specific set of features - eg. genes and QTLs associated with a specific phenotype, etc. rather than as a way to view all features on the genome. The features can hyperlink out to a detail page to enable to GViewer to be used as a navigation tool. In addition the bands on the chromosomes can link to defineable URL and new region selection sliders can be used to select a specific chromosome region and then link out to a genome browser for higher resolution information. Genome maps for Rat, Mouse, Human and C. elegans are provided but other genome maps can be easily created. Annotation data can be provided as static text files or produced as XML via server scripts. This tool is not GO-specific, but was built for the purpose of viewing GO annotation data. Platform: Online tool

Proper citation: Flash Gviewer (RRID:SCR_012870) Copy   

•   Source: SciCrunch Registry

http://www.cbcb.umd.edu/software/glimmer-mg/

A software system for finding genes in environmental shotgun DNA sequences.

Proper citation: Glimmer-MG (RRID:SCR_011932) Copy   

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http://www003.upp.so-net.ne.jp/pub/publications.html#sl

Software application for inkage disequilibrium grouping of single nucleotide polymorphisms (SNPs) reflecting haplotype phylogeny for efficient selection of tag SNPs. (entry from Genetic Analysis Software)

Proper citation: LDGROUP (RRID:SCR_006282) Copy   

•   Source: SciCrunch Registry

http://www.people.fas.harvard.edu/~junliu/em/em.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A haplotype inference program.

Proper citation: EM-DECODER (RRID:SCR_000023) Copy   

•   Source: SciCrunch Registry

http://www2.bsc.gwu.edu/bsc/oneproj.php?pkey=28

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Collect, store, and distribute genetic samples from cases and controls of type 1 diabetes and diabetic nephropathy for investigator-driven research into the genetic basis of diabetic nephropathy. As the risk of kidney complications in type 1 diabetes appears to have a considerable genetic component, this study assembled a large data resource for researchers attempting to identify causative genetic variants. The types of data collected allowed traditional case-control testing, a rapid and often powerful approach, and family-based analysis, a robust approach that is not influenced by population substructure.

Proper citation: Genetics of Kidneys in Diabetes (RRID:SCR_000133) Copy   

•   Source: SciCrunch Registry

http://lpg.nci.nih.gov/lpg_small/protocols/HapScope/

Software application that includes a comprehensive analysis pipeline and a sophisticated visualization tool for analyzing functionally annotated haplotypes. (entry from Genetic Analysis Software)

Proper citation: HAPSCOPE (RRID:SCR_000838) Copy   

•   Source: SciCrunch Registry

http://mlemire.freeshell.org/software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 6th,2023. Software application with implementation of the Sad statistic, more robust to transmission ratio distortion in the context of allele sharing (entry from Genetic Analysis Software)

Proper citation: GENEHUNTER SAD (RRID:SCR_000831) Copy   

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http://cedar.genetics.soton.ac.uk/pub/PROGRAMS/comds

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2022. Software application for combined segregation and linkage analysis, incorporating severity and diathesis. (entry from Genetic Analysis Software)

Proper citation: COMDS (RRID:SCR_000832) Copy   

•   Source: SciCrunch Registry

http://www.genetics.emory.edu/labs/epstein/software/chaplin/index.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022.Software application for identifying specific haplotypes or haplotype features that are associated with disease using genotype data from a case-control study. (entry from Genetic Analysis Software)

Proper citation: CHAPLIN (RRID:SCR_000833) Copy   

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http://compgen.rutgers.edu/crimap.shtml

Software application for constructing multilocus linkage map (entry from Genetic Analysis Software)

Proper citation: CRIMAP (RRID:SCR_000834) Copy   

•   Source: SciCrunch Registry

http://ki.se/ki/jsp/polopoly.jsp?d=29346&a=31576&l=en

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. PRACSIS (Prognosis and Risk in Acute Coronary Syndromes In Sweden) aims to study prognosis and its predictors in a consecutive series of patients with acute coronary syndrome (ACS). The study is comprised of patients between 18 and 80 years diagnosed at the coronary care unit at the Sahlgrenska University Hospital with unstable angina, non-ST-elevation MI or ST-elevation MI. Extensive information on medical history and blood samples for analyses of biochemical markers and genetic factors have been collected.

Proper citation: PRACSIS - Prognosis and Risk in Acute Coronary Syndromes In Sweden (RRID:SCR_000615) Copy   

•   Source: SciCrunch Registry

http://research.i2r.a-star.edu.sg:8080/kleisli/demos/pedigree/

Software application (entry from Genetic Analysis Software)

Proper citation: PEDIGREE-VISUALIZER (RRID:SCR_000842) Copy   

•   Source: SciCrunch Registry

http://vorlon.case.edu/~jxl175/haplotyping.html

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on August 23,2022. Software application for inferring haplotypes from genotypes on pedigree data (entry from Genetic Analysis Software)

Proper citation: PEDPHASE (RRID:SCR_000843) Copy   

•   Source: SciCrunch Registry

http://animalgene.umn.edu/locusmap/index.html

Software package designed for rapid linkage analysis and map construction of loci with a variety of inheritance modes. (entry from Genetic Analysis Software)

Proper citation: LOCUSMAP (RRID:SCR_000840) Copy   

•   Source: SciCrunch Registry

http://www-genome.wi.mit.edu/ftp/pub/software/rhmapper/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30, 2022. An interactive software program for radiation hybrid mapping (entry from Genetic Analysis Software)

Proper citation: RHMAPPER (RRID:SCR_000845) Copy   

•   Source: SciCrunch Registry

http://titan.biotec.uiuc.edu/bee/honeybee_project.htm

A database integrating data from the bee brain EST sequencing project with data from sequencing and gene research projects from other organisms, primarily the fruit fly Drosophila melanogaster. The goal of Bee-ESTdb is to provide updated information on the genes of the honey bee, currently using annotation primarily from flies to suggest cellular roles, biological functions, and evolutionary relationships. The site allows searches by sequence ID, EST annotations, Gene Ontology terms, Contig ID and using BLAST. Very nice resource for those interested in comparative genomics of brain. A normalized unidirectional cDNA library was made in the laboratory of Prof. Bento Soares, University of Iowa. The library was subsequently subtracted. Over 20,000 cDNA clones were partially sequenced from the normalized and subtracted libraries at the Keck Center, resulting in 15,311 vector-trimmed, high-quality, sequences with an average read length of 494 bp. and average base-quality of 41. These sequences were assembled into 8966 putatively unique sequences, which were tested for similarity to sequences in the public databases with a variety of BLAST searches. The Clemson University Genomics Institute is the distributor of these public domain cDNA clones. For information on how to purchase an individual clone or the entire collection, please contact www.genome.clemson.edu/orders/ or generobi (at) life.uiuc.edu.

Proper citation: Honey Bee Brain EST Project (RRID:SCR_002389) Copy   

•   Source: SciCrunch Registry