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http://www.bork.embl.de/j/

The main focus of this Computational Biology group is to predict function and to gain insights into evolution by comparative analysis of complex molecular data. The group currently works on three different scales: * genes and proteins, * protein networks and cellular processes, and * phenotypes and environments. They require both tool development and applications. Some selected projects include comparative gene, genome and metagenome analysis, mapping interactions to proteins and pathways as well as the study of temporal and spatial protein network aspects. All are geared towards the bridging of genotype and phenotype through a better understanding of molecular and cellular processes. The services - resources & tools, developed by Bork Group, are mainly designed and maintained for research & academic purposes. Most of services are published and documented in one or more papers. All our tools can be completely customized and integrated into your existing framework. This service is provided by the company biobyte solutions GmbH. Please visit their tools and services pages for full details and more information. Standard commercial licenses for our tools are also available through biobyte solutions GmbH. The group is partially associated with Max Delbr��ck Center for Molecular Medicine (MDC), Berlin.

Proper citation: EMBL - Bork Group (RRID:SCR_000810) Copy   

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https://github.com/feschottelab/REPCLASS

Tool for the classification of known transposable elements in eukaryotic genomes. It can be combined with ab initio repeat finding in order to recover contrasting transposable element landscapes between species.

Proper citation: REPCLASS (RRID:SCR_014654) Copy   

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https://gemini.readthedocs.io/en/latest/

Framework for exploring genetic variation in the context of the genome annotations available for the human genome. Users can load a VCF file into a database and each variant is automatically annotated by comparing it to several genome annotations from source such as ENCODE tracks, UCSC tracks, OMIM, dbSNP, KEGG, and HPRD.

Proper citation: GEMINI (RRID:SCR_014819) 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.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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https://esp.gs.washington.edu/

Project focused on understanding the contribution of rare genetic variation to heart, lung and blood disorders through the sequencing of well-phenotyped populations.

Proper citation: NHLBI Grand Opportunity Exome Sequencing Project (RRID:SCR_010798) 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.evocontology.org/site/Main/EvocOntologyDotOrg

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented September 6, 2016. Set of orthogonal controlled vocabularies that unifies gene expression data by facilitating a link between the genome sequence and expression phenotype information. The system associates labelled target cDNAs for microarray experiments, or cDNA libraries and their associated transcripts with controlled terms in a set of hierarchical vocabularies. eVOC consists of four orthogonal controlled vocabularies suitable for describing the domains of human gene expression data including Anatomical System, Cell Type, Pathology and Developmental Stage. The four core eVOC ontologies provide an appropriate set of detailed human terms that describe the sample source of human experimental material such as cDNA and SAGE libraries. These expression terms are linked to libraries and transcripts allowing the assessment of tissue expression profiles, differential gene expression levels and the physical distribution of expression across the genome. Analysis is currently possible using EST and SAGE data, with microarray data being incorporated. The eVOC data is increasingly being accepted as a standard for describing gene expression and eVOC ontologies are integrated with the Ensembl EnsMart database, the Alternate Transcript Diversity Project and the UniProt Knowledgebase. Several groups are currently working to provide shared development of this resource such that it is of maximum use in unifying transcript expression information.

Proper citation: eVOC (RRID:SCR_010704) Copy   

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http://beetlebase.org/

A centralized sequence database and community resource for Tribolium genetics, genomics and developmental biology containing genomic sequence scaffolds mapped to 10 linkage groups, genetic linkage maps, the official gene set, Reference Sequences from NCBI (RefSeq), predicted gene models, ESTs and whole-genome tiling array data representing several developmental stages. The current version of Beetlebase is built on the Tribolium castaneum 3.0 Assembly (Tcas 3.0) released by the Human Genome Sequencing Center at the Baylor College of Medicine. The database is constructed using the upgraded Generic Model Organism Database (GMOD) modules. The genomic data is stored in a PostgreSQL relational database using the Chado schema and visualized as tracks in GBrowse. The genetic map is visualized using the comparative genetic map viewer CMAP. To enhance search capabilities, the BLAST search tool has been integrated with the GMOD tools. Tribolium castaneum is a very sophisticated genetic model organism among higher eukaryotes. As the member of a primitive order of holometabolous insects, Coleoptera, Tribolium is in a key phylogenetic position to understand the genetic innovations that accompanied the evolution of higher forms with more complex development. Coleoptera is also the largest and most species diverse of all eukaryotic orders and Tribolium offers the only genetic model for the profusion of medically and economically important species therein. The genome sequences may be downloaded.

Proper citation: BeetleBase (RRID:SCR_001955) Copy   

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http://www.uib.no/en/cbu

An inter-department center that conducts bioinformatics research and expands the interface between bioinformatics and experimental biological and biomedical research. The unit is closely associated with the the Bioinformatics group at the Department of Informatics (II) and has tight links with the Sars Centre for Marine Molecular biology (SARS) and the Department of Molecular Biology (MBI). Six research groups are currently associated with CBU with projects that include sequence and structure analysis, molecular evolution, genome annotation and genomics data analysis. CBU also provides services and contributes to bioinformatics education primarily through training courses.

Proper citation: University of Bergen Computational Biology Unit (RRID:SCR_002970) Copy   

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