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http://www.ebi.ac.uk/parasites/parasite-genome.html

This website contains information about the genomic sequence of parasites. It also contains multiple search engines to search six frame translations of parasite nucleotide databases for motifs, parasite protein databases for motifs, and parasite protein databases for keywords and text terms. * Guide to Internet Access to Parasite Genome Information * Guide to web-based analysis tools * Parasite Genome BLAST Server: Search a range of parasite specific nucleotide sequence databases with your own sequence. * Parasite Proteome Keyword Search Facility: Search parasite protein databases for keywords and text terms * Parasite Proteome Motif Search Facility: Search parasite protein databases for motifs * Parasite Six Frame Translation Motif Search Facility: Search six frame translations of parasite nucleotide databases for motifs * Genome computing resources: A list of ftp and gopher sites where genome computing applications and other resources can be found.

Proper citation: Parasite genome databases and genome research resources (RRID:SCR_008150) Copy   

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http://www.hgsc.bcm.tmc.edu/content/bovine-genome-project

Downloadable files of the bos taurus genome. Draft assemblies available for download as contigs or linearized scaffolds of the genomic sequence of cow, Bos taurus, including the final draft assembly (7.1 coverage) and the two previous assemblies. The genome is sequenced to 6- to 8-fold sequence depth, with high-quality finished sequence in some areas. Accompanying EST and SNP analyses is also included. The bovine genome assembly and analysis and the study of cattle genetic history were published in April 24, 2009 issue of Science. The Human Genome Sequencing Center provides BLAST searches of the genome assemblies, either as contigs or as linearized chromosome sequences. The WGS sequence enriched BAC assemblies and the unassembled reads (sequencing reads that did not end up in the genome assembly) can also be searched by BLAST. Traces are available from the NCBI Trace Archive by using the link in the sidebar or by using NCBI MegaBLAST with a same species or cross species query.

Proper citation: Bovine Genome Project (RRID:SCR_008370) Copy   

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http://www.cshl.edu/

Non profit, private research and education institution that performs molecular and genetic research used to generate methods for better diagnostics and treatments for cancer and neurological diseases. Research of cancer causing genes and their respective signaling pathways, mutations and structural variations of the human genome that could cause neurodevelopmental and neurodegenerative illnesses such as autism, schizophrenia, and Alzheimer's and Parkinson's diseases and also research in plant genetics and quantitative biology.

Proper citation: Cold Spring Harbor Laboratory (RRID:SCR_008326) Copy   

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http://www.broad.mit.edu/mammals/dog

The genome of the domesticated dog, a close evolutionary relation to human, is a powerful new tool for understanding the human genome. Comparison of the dog with human and other mammals reveals key information about the structure and evolution of genes and genomes. The unique breeding history of dogs, with their extraordinary behavioral and physical diversity, offers the opportunity to find important genes underlying diseases shared between dogs and humans, such as cancer, diabetes, and epilepsy. The Canine Genome Sequencing Project produced a high-quality draft sequence of a female boxer named Tasha. By comparing Tasha with many other breeds, the project also compiled a comprehensive set of SNPs (single nucleotide polymorphisms) useful in all dog breeds. These closely spaced genomic landmarks are critical for disease mapping. By comparing the dog, rodent, and human lineages, researchers at the Broad Institute uncovered exciting new information about human genes, their evolution, and the regulatory mechanisms governing their expression. Using SNPs, researchers describe the strikingly different haplotype structure in dog breeds compared with the entire dog population. In addition, they show that by understanding the patterns of variation in dog breeds, scientists can design powerful gene mapping experiments for complex diseases that are difficult to map in human populations. Contribute Although the astounding generosity of Eli and Edythe L. Broad and several other venture philanthropists empowers our scientists to tackle many of the most important problems at the cutting edge of genomic medicine, there are many other critical challenges that they cannot yet pursue because of limited resources. We need additional visionary partners to join the Broads and the Broad Institute in transforming medicine with the power of genomics.

Proper citation: Dog Genome Project (RRID:SCR_008486) Copy   

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http://www.sanger.ac.uk/

Non profit research organization for genome sequences to advance understanding of biology of humans and pathogens in order to improve human health globally. Provides data which can be translated for diagnostics, treatments or therapies including over 100 finished genomes, which can be downloaded. Data are publicly available on limited basis, and provided more extensively upon request.

Proper citation: Wellcome Trust Sanger Institute; Hinxton; United Kingdom (RRID:SCR_011784) Copy   

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http://www.g-language.org/GenomeProjector/

A searchable database browser with zoomable user interface using Google Map API. Genome Projector currently contains 4 views: Genome map, Plasmid map, Pathway map, and DNA walk.

Proper citation: Genome Projector (RRID:SCR_011790) Copy   

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http://www.genestack.com

A universal collaborative platform for bioinformatics application development that allows users to store and share large data sets securely within and across organizations, with free access to public data from major databases. The platform includes open-source and proprietary genomics applications, working together independent of file formats. For developers an SDK, APIs and a marketplace are provided.

Proper citation: Genestack (RRID:SCR_011885) Copy   

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http://www.genboree.org/java-bin/EpigenomeAtlas/workbench.jsp?isPublic=yes&context=EpigenomeAtlas

Service where users are able to upload and store data, access bioinformatics tools, and perform analyses.

Proper citation: Genboree Workbench (RRID:SCR_011864) Copy   

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http://bioinfo-out.curie.fr/projects/snp_gap/

Software for automatic detection of absolute segmental copy numbers and genotype status in complex cancer genome profiles measured by single-nucleotide polymorphism (SNP) arrays. The method is based on pattern recognition of segmented and smoothed copy number and allelic imbalance profiles. The method performs well even for poor-quality data, low tumor content, and highly rearranged tumor genomes.

Proper citation: Genome Alteration Print (RRID:SCR_012016) Copy   

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http://www.hgvs.org

The Society aims to foster discovery and characterization of genomic variations including population distribution and phenotypic associations. We promote collection, documentation and free distribution of genomic variation information and associated clinical variations and endeavor to foster the development of the necessary methodology and informatics. Mission Statement To enhance human health through identification and characterization of changes in the genome that lead to susceptibility to illness. To this end, to collate the genomic information necessary for molecular diagnosis, research on basic mechanisms and design of treatments of human ailments. Society Journal Human Mutation is the Society journal. Members will receive a reduced subscription to the journal if they choose to subscribe. Meetings The Society holds two scientific meetings per year. One as a satellite to either the HUGO (Human Genome Organization) annual meeting or the ESHG (European Society of Human Genetics) annual meeting and one meeting is a satellite to the ASHG (American Society of Human Genetics annual meeting. The meetings are a forum for scientists to exchange ideas and form collaborations. Prominent speakers in the field are invited as well as a call for abstracts at large. The meetings are designed to update and increase knowledge of human genome variation and generally attract a stimulating and interesting collection of abstracts in all fields of human genome variation making it an ideal forum to share information and results. Past themes include: copy number variation, pathogenic or not?, pharmacogenomics, new DNA sequencing technologies, and genotype to pheontype relationships. We invite members and non-members alike to attend these meetings. The Society holds the Annual General Meeting of the members after the scientific meeting that is a satellite of the ASHG. Exhibitor''s booths The Society usually takes out an Exhibitor''s booth at the American & European Societies of Human Genetics annual meetings and sometimes the HUGO HGM meeting. GUIDELINES & RECOMMENDATIONS Members of the Society have formulated Guidelines & Recommendations on a number of topics, but especially for nomenclature of gene variations and guidelines on variation databases.

Proper citation: Human Genome Variation Society (RRID:SCR_012989) Copy   

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http://commonfund.nih.gov/GTEx/

Project to study human gene expression and regulation in multiple tissues, providing valuable insights into mechanisms of gene regulation and its disease related perturbations. Genetic variation between individuals will be examined for correlation with differences in gene expression level to identify regions of the genome that influence whether and how much a gene is expressed. Includes initiatives: Novel Statistical Methods for Human Gene Expression Quantitative Trait Loci (eQTL) Analysis ,Laboratory, Data Analysis, and Coordinating Center (LDACC), caHUB Acquisition of Normal Tissues in Support of GTEx Project.

Proper citation: Genotype-Tissue Expression (RRID:SCR_013042) Copy   

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http://www.ornl.gov/sci/techresources/Human_Genome/home.shtml

This resource gives information about the U.S. Human Genome Project, which was was a 13-year effort to to discover all the estimated 20,000-25,000 human genes and make them accessible for further biological study. The primary project goals were to: - identify all the approximately 20,000-25,000 genes in human DNA, - determine the sequences of the 3 billion chemical base pairs that make up human DNA, - store this information in databases, - improve tools for data analysis, - transfer related technologies to the private sector, and - address the ethical, legal, and social issues (ELSI) that may arise from the project. To help achieve these goals, researchers also studied the genetic makeup of several nonhuman organisms. These include the common human gut bacterium Escherichia coli, the fruit fly, and the laboratory mouse. These parallel studies helped to develop technology and interpret human gene function. Sponsors: The DOE Human Genome Program and the NIH National Human Genome Research Institute (NHGRI) together sponsored the U.S. Human Genome Project.

Proper citation: Human Genome Project Information (RRID:SCR_013028) Copy   

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https://bitbucket.org/nsegata/phylophlan/wiki/Home

Software pipeline for reconstructing highly accurate and resolved phylogenetic trees based on whole-genome sequence information. Pipeline is scalable to thousands of genomes and uses the most conserved 400 proteins for extracting the phylogenetic signal. PhyloPhlAn also implements taxonomic curation, estimation, and insertion operations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PhyloPhlAn (RRID:SCR_013082) Copy   

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http://genetics.bwh.harvard.edu/pph2/

Software tool which predicts possible impact of amino acid substitution on structure and function of human protein using straightforward physical and comparative considerations. PolyPhen-2 is new development of PolyPhen tool for annotating coding nonsynonymous SNPs.

Proper citation: PolyPhen: Polymorphism Phenotyping (RRID:SCR_013189) Copy   

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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   

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http://www.mrc-lmb.cam.ac.uk/genomes/dolop/

DOLOP is an exclusive knowledge base for bacterial lipoproteins by processing information from 510 entries to provide a list of 199 distinct lipoproteins with relevant links to molecular details. Features include functional classification, predictive algorithm for query sequences, primary sequence analysis and lists of predicted lipoproteins from 43 completed bacterial genomes along with interactive information exchange facility. This website along will have additional information on the biosynthetic pathway, supplementary material and other related figures. DOLOP also contains information and links to molecular details for about 278 distinct lipoproteins and predicted lipoproteins from 234 completely sequenced bacterial genomes. Additionally, the website features a tool that applies a predictive algorithm to identify the presence or absence of the lipoprotein signal sequence in a user-given sequence. The experimentally verified lipoproteins have been classified into different functional classes and more importantly functional domain assignments using hidden Markov models from the SUPERFAMILY database that have been provided for the predicted lipoproteins. Other features include: primary sequence analysis, signal sequence analysis, and search facility and information exchange facility to allow researchers to exchange results on newly characterized lipoproteins.

Proper citation: DOLOP: A Database of Bacterial Lipoproteins (RRID:SCR_013487) Copy   

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http://ctb.pku.edu.cn/main/SheGroup/Software/MED2.htm

A non-supervised gene prediction algorithm for prokaryotic genomes with multivariate entropy distance method.

Proper citation: MED (RRID:SCR_013403) Copy   

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http://www.plantagora.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. A web-based plant genome assembly simulation platform whose resources include out of the box scripts for analyzing assembly data, an on-demand web graphing tool to model your experiment, and a downloadable database with metrics and parameters from over 3,000 simulated genome assemblies.

Proper citation: Plantagora (RRID:SCR_001227) Copy   

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https://www.sanger.ac.uk/collaboration/sequencing-idd-regions-nod-mouse-genome/

Genetic variations associated with type 1 diabetes identified by sequencing regions of the non-obese diabetic (NOD) mouse genome and comparing them with the same areas of a diabetes-resistant C57BL/6J reference mouse allowing identification of single nucleotide polymorphisms (SNPs) or other genomic variations putatively associated with diabetes in mice. Finished clones from the targeted insulin-dependent diabetes (Idd) candidate regions are displayed in the NOD clone sequence section of the website, where they can be downloaded either as individual clone sequences or larger contigs that make up the accession golden path (AGP). All sequences are publicly available via the International Nucleotide Sequence Database Collaboration. Two NOD mouse BAC libraries were constructed and the BAC ends sequenced. Clones from the DIL NOD BAC library constructed by RIKEN Genomic Sciences Centre (Japan) in conjunction with the Diabetes and Inflammation Laboratory (DIL) (University of Cambridge) from the NOD/MrkTac mouse strain are designated DIL. Clones from the CHORI-29 NOD BAC library constructed by Pieter de Jong (Children's Hospital, Oakland, California, USA) from the NOD/ShiLtJ mouse strain are designated CHORI-29. All NOD mouse BAC end-sequences have been submitted to the International Nucleotide Sequence Database Consortium (INSDC), deposited in the NCBI trace archive. They have generated a clone map from these two libraries by mapping the BAC end-sequences to the latest assembly of the C57BL/6J mouse reference genome sequence. These BAC end-sequence alignments can then be visualized in the Ensembl mouse genome browser where the alignments of both NOD BAC libraries can be accessed through the Distributed Annotation System (DAS). The Mouse Genomes Project has used the Illumina platform to sequence the entire NOD/ShiLtJ genome and this should help to position unaligned BAC end-sequences to novel non-reference regions of the NOD genome. Further information about the BAC end-sequences, such as their alignment, variation data and Ensembl gene coverage, can be obtained from the NOD mouse ftp site.

Proper citation: Sequencing of Idd regions in the NOD mouse genome (RRID:SCR_001483) Copy   

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http://ccr.coriell.org/Sections/Collections/NHGRI/?SsId=11

DNA samples and cell lines from fifteen populations, including the samples used for the International HapMap Project, the HapMap 3 Project and the 1000 Genomes Project (except for the CEPH samples). All of the samples were contributed with consent to broad data release and to their use in many future studies, including for extensive genotyping and sequencing, gene expression and proteomics studies, and all other types of genetic variation research. NHGRI led the contribution of the NIH to the International HapMap Project, which developed a haplotype map of the human genome. This haplotype map, called the HapMap is a publicly available tool that allows researchers to find genes and genetic variations that affect health and disease. The samples from four populations used to develop the HapMap were initially housed in the Human Genetic Cell Repository of the National Institute of General Medical Sciences (NIGMS). Except for the Utah CEPH samples that were in the NIGMS Repository before the initiation of the HapMap Project and remain there, the NHGRI Repository now houses all of the HapMap samples. The NHGRI repository also houses the extended set of HapMap samples, which includes additional samples from the HapMap populations and samples from seven additional populations. All of the samples were collected with extensive community engagement, including discussions with members of the donor communities about the ethical and social implications of human genetic variation research. These samples were studied as part of the HapMap 3 Project. The NHGRI repository also houses the samples for the International 1000 Genomes Project. This Project is lightly sequencing genome-wide 2500 samples from 27 populations. This project aims to provide a detailed map of human genetic variation, including common and rare SNPs and structural variants. This map will allow more precise localization of genomic regions that contribute to health and disease. The 1000 Genomes Project includes many of the samples from the HapMap and extended set of HapMap samples, as well as samples being collected from additional populations. Currently, samples from five additional populations are available; the others will become available during 2011 and 2012. No identifying or phenotypic information is available for the samples. Donors gave broad consent for use of the samples, including for genotyping, sequencing, and cellular phenotype studies. Samples collected from other populations for the study of human genetic variation may be added to the collection in the future. The NHGRI Repository distributes high quality lymphoblastoid cell lines and DNA from the samples to researchers. DNA is provided in plates or panels of 70 to 100 samples or as individual samples. Cell cultures and DNA samples are distributed only to qualified professional persons who are associated with recognized research, medical, educational, or industrial organizations engaged in health-related research or health delivery.

Proper citation: NHGRI Sample Repository for Human Genetic Research (RRID:SCR_004528) Copy   

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