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Software application as an integrated web resource of marmoset biological data. Used to find genomic, expression and alternative splicing data to facilitate the study of animal model for neuropsychiatric and social behavior research and to support biological analyses such as functional (ontology) enrichment analysis and protein-protein-network.
Proper citation: CajaDB (RRID:SCR_016506) Copy
https://genome.jgi.doe.gov/programs/fungi/1000fungalgenomes.jsf
Web application to provide genomic information for fungi. Includes sequenced fungal genomes, those in progress, and selected nominations. Nomination of new species for genome sequencing in the families or only one reference genome possible after providing DNA/RNA samples for their sequencing. Used to explore the diversity of fungi important for energy and the environment.
Proper citation: 1000 Fungal Genome Project (RRID:SCR_016463) Copy
Database and information retrieval, analysis, and visualization system for microbial resources to help culture collections to manage, disseminate and share the information related to their holdings. Provides an interface for the scientific and industrial communities to access the microbial resource information.
Proper citation: Global Catalogue of Microorganisms (RRID:SCR_016460) Copy
Collection of curated papillomavirus genomic sequences, accompanied by web-based sequence analysis tools. Database and web applications support the storage, annotation, analysis, and exchange of information.
Proper citation: PaVE (RRID:SCR_016599) Copy
https://github.com/INTABiotechMJ/MITE-Tracker
Open source software tool for identifying miniature inverted repeat transposable elements in large genomes. Used to process large scale genomes, to find and classify MITEs using an efficient alignment strategy to retrieve nearby inverted repeat sequences.
Proper citation: MITE-Tracker (RRID:SCR_017030) Copy
Core to assist with analyzing and interpreting data produced by genomic technologies.
Proper citation: University of North Carolina Charlotte Bioinformatics Services Division (RRID:SCR_017182) Copy
https://www.cityofhope.org/research/shared-resources/integrative-genomics-and-bioinformatics
Core provides genomic and bioinformatics services to City of Hope Comprehensive Cancer Center (COHCCC) investigators.
Proper citation: City of Hope National Medical Center Integrative Genomics and Bioinformatics Core Facility (RRID:SCR_017188) Copy
https://github.com/ZSI-Bio/bdg-sequila
Software tool for genomic intervals querying and processing built on top of Apache Spark. Elastic, fast and scalable SQL oriented solution for processing and querying genomic intervals.
Proper citation: SeQuiLa (RRID:SCR_017220) Copy
https://www.bmh.manchester.ac.uk/research/facilities/bioinformatics/
Core provides assistance in integrative analysis of genomic datasets to support faculty.
Proper citation: University of Manchester Bioinformatics Core Facility (RRID:SCR_017171) Copy
Consortium to bring together clinicians, pathologists, researchers, and biotech innovators to create scalable network of stakeholders interested in helping patients with glomerular kidney disease. Makes collective expertise of its members available for discussion of individual cases, provides infrastructure for biomarker studies, enables genomic research, and facilitates clinical trials.
Proper citation: Glomerular Disease Study & Trial Consortium (RRID:SCR_017264) Copy
Portal to facilitate integration and computing on and across large datasets generated by NHGRI programs, as well as initiatives funded by National Institutes of Health or by other agencies that support human genomics research. Resource for genomic scientific community, that leverages cloud based infrastructure for democratizing genomic data access, sharing and computing across large genomic, and genomic related data sets. Component of federated data ecosystem, and is expected to collaborate and integrate with other genomic data resources through adoption of FAIR (Findable, Accessible, Interoperable, Reusable) principles, as their specifications emerge from scientific community. Will provide collaborative environment, where datasets and analysis workflows can be shared within consortium and be prepared for public release to broad scientific community through AnVIL user interfaces.
Proper citation: Analysis, Visualization, and Informatics Lab-space (AnVIL) (RRID:SCR_017469) Copy
https://bioconductor.org/packages/TCGAbiolinks/
Software R Bioconductor package for integrative analysis with TCGA data.TCGAbiolinks is able to access National Cancer Institute Genomic Data Commons thorough its GDC Application Programming Interface to search, download and prepare relevant data for analysis in R.
Proper citation: TCGAbiolinks (RRID:SCR_017683) Copy
https://github.com/esctrionsit/snphub
Web Shiny-based server framework for retrieving, analyzing and visualizing large genomic variations data.
Proper citation: SnpHub (RRID:SCR_018177) Copy
http://www.imperial.ac.uk/research/animallectins
Resource presents information about animal lectins involved in various sugar recognition processes.
Proper citation: genomics resource for animal lectins (RRID:SCR_018122) Copy
http://www.ebi.ac.uk/expressionprofiler/
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. The EP:GO browser is built into EBI's Expression Profiler, a set of tools for clustering, analysis and visualization of gene expression and other genomic data. With it, you can search for GO terms and identify gene associations for a node, with or without associated subnodes, for the organism of your choice.
Proper citation: Expression Profiler (RRID:SCR_005821) Copy
ProPortal is a database containing genomic, metagenomic, transcriptomic and field data for the marine cyanobacterium Prochlorococcus. Our goal is to provide a source of cross-referenced data across multiple scales of biological organization--from the genome to the ecosystem--embracing the full diversity of ecotypic variation within this microbial taxon, its sister group, Synechococcus and phage that infect them. The site currently contains the genomes of 13 Prochlorococcus strains, 11 Synechococcus strains and 28 cyanophage strains that infect one or both groups. Cyanobacterial and cyanophage genes are clustered into orthologous groups that can be accessed by keyword search or through a genome browser. Users can also identify orthologous gene clusters shared by cyanobacterial and cyanophage genomes. Gene expression data for Prochlorococcus ecotypes MED4 and MIT9313 allow users to identify genes that are up or downregulated in response to environmental stressors. In addition, the transcriptome in synchronized cells grown on a 24-h light-dark cycle reveals the choreography of gene expression in cells in a ''natural'' state. Metagenomic sequences from the Global Ocean Survey from Prochlorococcus, Synechococcus and phage genomes are archived so users can examine the differences between populations from diverse habitats. Finally, an example of cyanobacterial population data from the field is included.
Proper citation: ProPortal (RRID:SCR_006112) Copy
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
http://chgr.mc.vanderbilt.edu/page/gist
Software package to test if a marker can account in part for the linkage signal in its region. There are two versions of the software: Windows and Linux/Unix.
Proper citation: Genotype-IBD Sharing Test (RRID:SCR_006257) Copy
http://genetrail.bioinf.uni-sb.de/
A web-based application that analyzes gene sets for statistically significant accumulations of genes that belong to some functional category. Considered category types are: KEGG Pathways, TRANSPATH Pathways, TRANSFAC Transcription Factor, GeneOntology Categories, Genomic Localization, Protein-Protein Interactions, Coiled-coil domains, Granzyme-B clevage sites, and ELR/RGD motifs. The web server provides two statistical approaches, "Over-Representation Analysis" (ORA) comparing a reference set of genes to a test set, and "Gene Set Enrichment Analysis" (GSEA) scoring sorted lists of genes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: GeneTrail (RRID:SCR_006250) Copy
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
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