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https://cghub.ucsc.edu/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. A secure repository for storing, cataloging, and accessing cancer genome sequences, alignments, and mutation information from the Cancer Genome Atlas (TCGA) consortium and related projects. CGHub gives scientific researchers the statistical power of large cancer genome datasets to attack the molecular complexity of cancer.

Proper citation: Cancer Genomics Hub (RRID:SCR_002657) Copy   

•   Source: SciCrunch Registry

http://bioweb.ensam.inra.fr/esther

Database and tools for analysis of protein and nucleic acid sequences belonging to superfamily of alpha/beta hydrolases homologous to cholinesterases. Covers multiple species, including human, mouse caenorhabditis and drosophila., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ESTHER (RRID:SCR_002621) Copy   

•   Source: SciCrunch Registry

http://www.flymine.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Integrated database of genomic, expression and protein data for Drosophila, Anopheles, C. elegans and other organisms. You can run flexible queries, export results and analyze lists of data. FlyMine presents data in categories, with each providing information on a particular type of data (for example Gene Expression or Protein Interactions). Template queries, as well as the QueryBuilder itself, allow you to perform searches that span data from more than one category. Advanced users can use a flexible query interface to construct their own data mining queries across the multiple integrated data sources, to modify existing template queries or to create your own template queries. Access our FlyMine data via our Application Programming Interface (API). We provide client libraries in the following languages: Perl, Python, Ruby and & Java API

Proper citation: FlyMine (RRID:SCR_002694) Copy   

•   Source: SciCrunch Registry

http://www.genomesonline.org/

Database of information regarding genome and metagenome sequencing projects, and their associated metadata, around the world. It also provides information related to organism properties such as phenotype, ecotype and disease. Both complete and ongoing projects, along with their associated metadata, can be accessed. Users can also register, annotate and publish genome and metagenome data.

Proper citation: Genomes Online Database (RRID:SCR_002817) Copy   

•   Source: SciCrunch Registry

http://genespeed.ccf.org/home/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. Database and customized tools to study the PFAM protein domain content of the transcriptome for all expressed genes of Homo sapiens, Mus musculus, Drosophila melanogaster, and Caenorhabditis elegans tethered to both a genomics array repository database and a range of external information resources. GeneSpeed has merged information from several existing data sets including the Gene Ontology Consortium, InterPro, Pfam, Unigene, as well as micro-array datasets. GeneSpeed is a database of PFAM domain homology contained within Unigene. Because Unigene is a non-redundant dbEST database, this provides a wide encompassing overview of the domain content of the expressed transcriptome. We have structured the GeneSpeed Database to include a rich toolset allowing the investigator to study all domain homology, no matter how remote. As a result, homology cutoff score decisions are determined by the scientist, not by a computer algorithm. This quality is one of the novel defining features of the GeneSpeed database giving the user complete control of database content. In addition to a domain content toolset, GeneSpeed provides an assortment of links to external databases, a unique and manually curated Transcription Factor Classification list, as well as links to our newly evolving GeneSpeed BetaCell Database. GeneSpeed BetaCell is a micro-array depository combined with custom array analysis tools created with an emphasis around the meta analysis of developmental time series micro-array datasets and their significance in pancreatic beta cells.

Proper citation: GeneSpeed- A Database of Unigene Domain Organization (RRID:SCR_002779) Copy   

•   Source: SciCrunch Registry

http://www.greenphyl.org/

A database designed for plant comparative and functional genomics based on complete genomes. It comprises complete proteome sequences from the major phylum of plant evolution. The clustering of these proteomes was performed to define a consistent and extensive set of homeomorphic plant families. Based on this, lists of gene families such as plant or species specific families and several tools are provided to facilitate comparative genomics within plant genomes. The analyses follow two main steps: gene family clustering and phylogenomic analysis of the generated families. Once a group of sequences (cluster) is validated, phylogenetic analyses are performed to predict homolog relationships such as orthologs and ultraparalogs.

Proper citation: GreenPhylDB (RRID:SCR_002834) Copy   

•   Source: SciCrunch Registry

http://www.ambystoma.org/

Portal that supports Ambystoma-related research and educational efforts. It is composed of several resources: Salamander Genome Project, Ambystoma EST Database, Ambystoma Gene Collection, Ambystoma Map and Marker Collection, Ambystoma Genetic Stock Center, and Ambystoma Research Coordination Network.

Proper citation: Sal-Site (RRID:SCR_002850) Copy   

•   Source: SciCrunch Registry

http://cbio.mskcc.org/

Computational biology research at Memorial Sloan-Kettering Cancer Center (MSKCC) pursues computational biology research projects and the development of bioinformatics resources in the areas of: sequence-structure analysis; gene regulation; molecular pathways and networks, and diagnostic and prognostic indicators. The mission of cBio is to move the theoretical methods and genome-scale data resources of computational biology into everyday laboratory practice and use, and is reflected in the organization of cBio into research and service components ~ the intention being that new computational methods created through the process of scientific inquiry should be generalized and supported as open-source and shared community resources. Faculty from cBio participate in graduate training provided through the following graduate programs: * Gerstner Sloan-Kettering Graduate School of Biomedical Sciences * Graduate Training Program in Computational Biology and Medicine Integral to much of the research and service work performed by cBio is the creation and use of software tools and data resources. The tools that we have created and utilize provide evidence of our involvement in the following areas: * Cancer Genomics * Data Repositories * iPhone & iPod Touch * microRNAs * Pathways * Protein Function * Text Analysis * Transcription Profiling

Proper citation: Computational Biology Center (RRID:SCR_002877) Copy   

•   Source: SciCrunch Registry

http://www.gabipd.org/

Database that collects, integrates and links all relevant primary information from the GABI plant genome research projects and makes them accessible via internet. Its purpose is to support plant genome research in Germany, to yield information about commercial important plant genomes, and to establish a scientific network within plant genomic research.
GreenCards is the main interface for text based retrieval of sequence, SNP, mapping data etc. Sharing and interchange of data among collaborating research groups, industry and the patent- and licensing agency are facilitated.
* GreenCards: Text based search for sequence, mapping, SNP data etc. * Maps: Visualization of genetic or physical maps. * BLAST: Secure BLAST search against different public databases or non-public sequence data stored in GabiPD. * Proteomics: View interactive 2D-gels and view or download information for identified protein spots. Registered users can submit data via secure file upload.

Proper citation: Gabi Primary Database (RRID:SCR_002755) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/annotation/genome/magnaporthe_comparative/MultiHome.html

The Magnaporthe comparative genomics database provides accesses to multiple fungal genomes from the Magnaporthaceae family to facilitate the comparative analysis. As part of the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies of Gaeumannomyces graminis var. tritici and M. poae. It provides users the tools to BLAST search, browse genome regions (to retrieve DNA, find clones, and graphically view sequence regions), and provides gene indexes and genome statistics. We were funded to attempt 7x sequence coverage comprising paired end reads from plasmids, Fosmids and BACs. Our strategy involves Whole Genome Shotgun (WGS) sequencing, in which sequence from the entire genome is generated and reassembled. Our specific aims are as follows: 1. Generate and assemble sequence reads yielding 7X coverage of the Magnaporthe oryzae genome through whole genome shotgun sequencing. 2. Generate and incorporate BAC and Fosmid end sequences into the genome assembly to provide a paired-end of average every 2 kb. 3. Integrate the genome sequence with existing physical and genetic map information. 4. Perform automated annotation of the sequence assembly. 5. Distribute the sequence assembly and results of our annotation and analysis through a freely accessible, public web server and by deposition of the sequence assembly in GenBank.

Proper citation: Magnaporthe comparative Database (RRID:SCR_003079) Copy   

•   Source: SciCrunch Registry

http://cgap.nci.nih.gov/

Project to determine the gene expression profiles of normal, precancer, and cancer cells, whose generated resources are available to the cancer community. Interconnected modules provide access to all CGAP data, bioinformatic analysis tools, and biological resources allowing the user to find in silico answers to biological questions in a fraction of the time it once took in the laboratory. * Genes * Tissues * Pathways * RNAi * Chromosomes * SAGE Genie * Tools

Proper citation: Cancer Genome Anatomy Project (RRID:SCR_003072) Copy   

•   Source: SciCrunch Registry

http://resexomedb.bioinf-dz.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. An online catalog for whole-exome sequencing (WES) results including mutations and gene-disease associations identified by WES. It is browsable and searchable by mutation, gene, study or publication. In addition, it centralizes all publications, software, platforms related to exome / whole genome sequencing.

Proper citation: resExomeDB (RRID:SCR_003224) Copy   

•   Source: SciCrunch Registry

http://bibiserv.techfak.uni-bielefeld.de/dialign/

Tool for multiple sequence alignment using various sources of external information that is particularly useful to detect local homologies in sequences with low overall similarity. While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing entire segments of the sequences. No gap penalty is used. This approach can be used for both global and local alignment, but it is particularly successful in situations where sequences share only local homologies. Several versions of DIALIGN are available online at GOBICS, http://dialign.gobics.de/

Proper citation: DIALIGN (RRID:SCR_003041) Copy   

•   Source: SciCrunch Registry

http://www.nematodes.org/

Nematode & Neglected Genomics (at) The Blaxter Lab is a nematode related portal including databases and services. Resources include genomic and transcriptomic databases for nematodes and other metazoan phyla and freely downloadable software tools for expressed sequence tag analysis, DNA barcode analysis and phylogenomics. Major categories include: * GenePool * 959 Nematode Genomes * Teaching * Research Projects * Bioinformatics Software Tools * Lab Personnel * Lab Wiki * Genomics Databases * NEMBASE4 * Tardigrada: Hypsibius dujardini * Earthworm: Lumbricus rubellus * MolluscDB * ArthropodDB * other Neglected Genomes

Proper citation: nematodes.org (RRID:SCR_003267) Copy   

•   Source: SciCrunch Registry

http://plantgrn.noble.org/LegumeIP/

LegumeIP is an integrative database and bioinformatics platform for comparative genomics and transcriptomics to facilitate the study of gene function and genome evolution in legumes, and ultimately to generate molecular based breeding tools to improve quality of crop legumes. LegumeIP currently hosts large-scale genomics and transcriptomics data, including: * Genomic sequences of three model legumes, i.e. Medicago truncatula, Glycine max (soybean) and Lotus japonicus, including two reference plant species, Arabidopsis thaliana and Poplar trichocarpa, with the annotation based on UniProt TrEMBL, InterProScan, Gene Ontology and KEGG databases. LegumeIP covers a total 222,217 protein-coding gene sequences. * Large-scale gene expression data compiled from 104 array hybridizations from L. japonicas, 156 array hybridizations from M. truncatula gene atlas database, and 14 RNA-Seq-based gene expression profiles from G. max on different tissues including four common tissues: Nodule, Flower, Root and Leaf. * Systematic synteny analysis among M. truncatula, G. max, L. japonicus and A. thaliana. * Reconstruction of gene family and gene family-wide phylogenetic analysis across the five hosted species. LegumeIP features comprehensive search and visualization tools to enable the flexible query on gene annotation, gene family, synteny, relative abundance of gene expression.

Proper citation: LegumeIP (RRID:SCR_008906) Copy   

•   Source: SciCrunch Registry

http://hymenopteragenome.org/beebase/

Gene sequences and genomes of Bombus terrestris, Bombus impatiens, Apis mellifera and three of its pathogens, that are discoverable and analyzed via genome browsers, blast search, and apollo annotation tool. The genomes of two additional species, Apis dorsata and A. florea are currently under analysis and will soon be incorporated.BeeBase is an archive and will not be updated. The most up-to-date bee genome data is now available through the navigation bar on the HGD Home page.

Proper citation: BeeBase (RRID:SCR_008966) Copy   

•   Source: SciCrunch Registry

http://rgd.mcw.edu/rgdCuration/?module=portal&func=show&name=renal

An integrated resource for information on genes, QTLs and strains associated with a variety of kidney and renal system conditions such as Renal Hypertension, Polycystic Kidney Disease and Renal Insufficiency, as well as Kidney Neoplasms.

Proper citation: Renal Disease Portal (RRID:SCR_009030) Copy   

•   Source: SciCrunch Registry

http://www.cbil.upenn.edu/cgi-bin/tess/tess

TESS is a web tool for predicting transcription factor binding sites in DNA sequences. It can identify binding sites using site or consensus strings and positional weight matrices from the TRANSFAC, JASPAR, IMD, and our CBIL-GibbsMat database. You can use TESS to search a few of your own sequences or for user-defined CRMs genome-wide near genes throughout genomes of interest. Search for CRMs Genome-wide: TESS now has the ability to search whole genomes for user defined CRMs. Try a search in the AnGEL CRM Searches section of the navigation bar.. You can search for combinations of consensus site sequences and/or PWMs from TRANSFAC or JASPAR. Search DNA for Binding Sites: TESS also lets you search through your own sequence for TFBS. You can include your own site or consensus strings and/or weight matrices in the search. Use the Combined Search under ''Site Searches'' in the menu or use the box for a quick search. TESS assigns a TESS job number to all sequence search jobs. The job results are stored on our server for a period of time specified in the search submit form. During this time you may recall the search results using the form on this page. TESS can also email results to you as a tab-delimited file suitable for loading into a spreadsheet program. Query for Transcription Factor Info: TESS also has data browsing and querying capabilities to help you learn about the factors that were predicted to bind to your sequence. Use the Query TRANSFAC or Query Matrices links above or use the search interface provided from the home page.

Proper citation: TESS: Transcription Element Search System (RRID:SCR_010739) Copy   

•   Source: SciCrunch Registry

http://jjwanglab.org/snvrap

The web portal provides comprehensive local database of human genome variants with a user-friendly web page that provides a one-stop annotating and funtonal prediction service which is both convenient and up-to-date. A query can be accepted as either a dbSNP Id or a chromosomal location and our system will instantly provide all the annotation information in an interactive LD panel. The system can also simultaneously prioritize this variant based on additive effect mode by corresponding annotation information and evaluate the variant effect that is then displayed in a prioritization tree. Furthermore, cohort sequencing continuously produces lots of un-annotated variants such as rare variants or de novo variants, and our system can even fit this data by accepting genomic coordinates (hg19) to offer maximal annotations. Main Functions Over 40 up-to-date annotation items for human single nucleotide variations; Functional prediction for different types of variants; Dynamic LD panel for both HapMap and 1000 Genomes Project populations; Prioritization score and tree viewer based on variant functional model.

Proper citation: SNVrap (RRID:SCR_010512) Copy   

•   Source: SciCrunch Registry

http://bio-bwa.sourceforge.net/

Software for aligning sequencing reads against large reference genome. Consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. First for sequence reads up to 100bp, and other two for longer sequences ranged from 70bp to 1Mbp.

Proper citation: BWA (RRID:SCR_010910) Copy   

•   Source: SciCrunch Registry