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http://ekhidna.biocenter.helsinki.fi/dali_server

Network service for comparing protein structures in 3D. You submit the coordinates of a query protein structure and Dali compares them against those in the Protein Data Bank (PDB). You receive an email notification when the search has finished. In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences. Requests can also be submitted by e-mail to dali-server at helsinki dot fi. The body of the e-mail message must contain atomic coordinates in PDB format. If you want to know the structural neighbours of a protein already in the Protein Data Bank (PDB), you can find them in the Dali Database. If you want to superimpose two particular structures, you can do it in the pairwise DaliLite server. Academic users may download the DaliLite program for local use.

Proper citation: Dali Server (RRID:SCR_013433) Copy   

•   Source: SciCrunch Registry

http://mobyle.pasteur.fr/

A portal for bioinformatics analyses, including the following: alignment assembly database display genetics hmm information nucleic phylogeny protein sequence structure

Proper citation: Mobyle@Pasteur (RRID:SCR_013089) Copy   

•   Source: SciCrunch Registry

http://www.functionalglycomics.org

This Gateway is a collaboration between the Consortium for Functional Glycomics (CFG) and Nature Publishing Group (NPG), providing a comprehensive resource for functional glycomics research. Use this site to stay up-to-date on glycomics news, request CFG resources, and search databases of glycan-binding proteins, glycan structures, and glycosyltransferases. The Functional Glycomics Update provides a one-stop overview of the latest research in glycobiology for specialists and non-specialists alike. It is updated monthly to bring you the latest news and selected highlights from Nature journals. In addition, it will provide two featured articles a month on the most relevant advances in the field published in NPG and other top journals. By collating new articles into a key worded research library, we hope to provide a continuously updated and broad overview of the field. Sponsor. The CFG is a large international research initiative funded by NIGMS to elucidate the roles of carbohydrate-protein interactions in cell communication at the cell surface.

Proper citation: Functional Glycomics Research (RRID:SCR_013337) Copy   

•   Source: SciCrunch Registry

http://golgi.unmc.edu/ptarget/

pTARGET is a computational method to predict the subcellular localization of only eukaryotic proteins from animal species that include fungi and metazoans. Predictions are carried out based on the occurrence patterns of protein functional domains and the amino acid compositional differences in proteins from different subcellular locations. This method can predict proteins targeted to nine distinct subcellular locations that include cytoplasm, endoplasmic reticulum, extracellular/secreted, Golgi, lysosomes, mitochondria, nucleus, peroxysomes and plasma membrane. Current predictions are based on Pfam database version 19.0. Datasets used for developing pTarget method are available., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: pTARGET (RRID:SCR_013458) Copy   

•   Source: SciCrunch Registry

http://tgrc.ucdavis.edu/

Genebank of wild relatives, monogenic mutants and miscellaneous genetic stocks of tomato. TGRC offers seed samples for free to researchers worldwide.

Proper citation: C.M. Rick Tomato Genetic Resources Center (RRID:SCR_014954) Copy   

•   Source: SciCrunch Registry

http://www.vtk.org

Cross-platform visualization software system for 3D computer graphics, image processing, and data visualization. Various visualization algorithms and advanced modeling techniques are supported within VTK, as well as parallel processing and interoperability with select databases.

Proper citation: VTK (RRID:SCR_015013) Copy   

•   Source: SciCrunch Registry

http://burgundy.cmmt.ubc.ca/cgi-bin/RAVEN/a?rm=home

Tool to search for putative regulatory genetic variation in your favorite gene. Single nucleotide polymorphisms (SNPs) (from dbSNP and user defined) are analyzed for overlap with potential transcription factor binding sites (TFBS) and phylogenetic footprinting using UCSC phastCons scores from multiple alignments of 8 vertebrate genomes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: RAVEN (RRID:SCR_001937) Copy   

•   Source: SciCrunch Registry

http://www.patricbrc.org/portal/portal/patric/Home

A Bioinformatics Resource Center bacterial bioinformatics database and analysis resource that provides researchers with an online resource that stores and integrates a variety of data types (e.g. genomics, transcriptomics, protein-protein interactions (PPIs), three-dimensional protein structures and sequence typing data) and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes, currently more than 10 000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. The PATRIC project includes three primary collaborators: the University of Chicago, the University of Manchester, and New City Media. The University of Chicago is providing genome annotations and a PATRIC end-user genome annotation service using their Rapid Annotation using Subsystem Technology (RAST) system. The National Centre for Text Mining (NaCTeM) at the University of Manchester is providing literature-based text mining capability and service. New City Media is providing assistance in website interface development. An FTP server and download tool are available.

Proper citation: Pathosystems Resource Integration Center (RRID:SCR_004154) Copy   

•   Source: SciCrunch Registry

http://www.theseed.org/wiki/Home_of_the_SEED

The SEED is a framework to support comparative analysis and annotation of genomes. The cooperative effort focuses on the development of the comparative genomics environment and, more importantly, on the development of curated genomic data. Curation of genomic data (annotation) is done via the curation of subsystems by an expert annotator across many genomes, not on a gene by gene basis. From the curated subsystems we extract a set of freely available protein families (FIGfams). These FIGfams form the core component of our RAST automated annotation technology. Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free RAST-Server (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the Metagenomics-RAST-Server freely available. We also provide a SEED-Viewer that allows read-only access to the latest curated data sets. We currently have 58 Archaea, 902 Bacteria, 562 Eukaryota, 1254 Plasmids and 1713 Viruses in our database. All tools and datasets that make up the SEED are in the public domain and can be downloaded at ftp://ftp.theseed.org

Proper citation: SEED (RRID:SCR_002129) Copy   

•   Source: SciCrunch Registry

http://www.predictprotein.org/

Web application for sequence analysis and the prediction of protein structure and function. The user interface intakes protein sequences or alignments and returned multiple sequence alignments, motifs, and nuclear localization signals., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.

Proper citation: Predictions for Entire Proteomes (RRID:SCR_002803) Copy   

•   Source: SciCrunch Registry

http://regulondb.ccg.unam.mx/

Database on transcriptional regulation in Escherichia coli K-12 containing knowledge manually curated from original scientific publications, complemented with high throughput datasets and comprehensive computational predictions. Graphic and text-integrated environment with friendly navigation where regulatory information is always at hand. They provide integrated views to understand as well as organized knowledge in computable form. Users may submit data to make it publicly available.

Proper citation: RegulonDB (RRID:SCR_003499) Copy   

•   Source: SciCrunch Registry

http://www.proteomexchange.org

A data repository for proteomic data sets. The ProteomeExchange consortium, as a whole, aims to provide a coordinated submission of MS proteomics data to the main existing proteomics repositories, as well as to encourage optimal data dissemination. ProteomeXchange provides access to a number of public databases, and users can access and submit data sets to the consortium's PRIDE database and PASSEL/PeptideAtlas.

Proper citation: ProteomeXchange (RRID:SCR_004055) Copy   

•   Source: SciCrunch Registry

http://www.carmen.org.uk/

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on January 14, 2023. Infrastructure for sharing data, tools and services, this virtual research environment (VRE) supports e-Neuroscience and is designed to provide services for data and processing of that data. While the system is initially focused on electrophysiology data (neural activity recordings are the primary data types), it is equally applicable to many domains outside neuroscience. The Portal Provides: * User login and customization. * Data upload/download. * Data handling including custom permissions for public, shared or private data. * The ability to invoke custom public, shared or private services that consume and produce data. For example, it would allow spike series to be run through a sorter, producing new data representing the sorted spikes. * The ability to host services written in a number of languages including, but not limited to Matlab, R, Python, Perl, Java. * A system to support metadata for data objects, which provides extensive support for entering metadata at the point of upload, and allows the generation of metadata from services to provide provenance information. * The ability to invoke additional visualization for the data, for example, via the Signal Data Explorer. A core part is the development of: (i) minimum reporting guidelines for annotation of data and other computational resources for the purpose of sharing, and; (ii) intermediate formats and APIs for translation between proprietary and bespoke data types. These recommendations are being implemented and the global community is encouraged both to engage in their specification and make use of them for their own data sharing systems. * MINI: Minimum Information about a Neuroscience Investigation - This framework represents the formalized opinion of the CARMEN consortium and its associates, and identifies the minimum reporting information required to support the use of electrophysiology in a neuroscience study, for submission to the CARMEN system. * NDTF: Neurophysiology Data Translation Format - This framework provides a vendor-independent mechanism for translating between raw and processed neurphysiology data in the form of time and image series. They are implementing NDTF in CARMEN but it may also be useful for third party applications.

Proper citation: Code Analysis Repository and Modelling for e-Neuroscience (RRID:SCR_002795) Copy   

•   Source: SciCrunch Registry

http://hcv.lanl.gov/

The Hepatitis C Virus (HCV) Database Project strives to present HCV-associated genetic and immunologic data in a user-friendly way, by providing access to the central database via web-accessible search interfaces and supplying a number of analysis tools.

Proper citation: HCV Databases (RRID:SCR_002863) Copy   

•   Source: SciCrunch Registry

https://github.com/

A web-based hosting service for software development projects that use the Git revision control system offering powerful collaboration, code review, and code management. It offers both paid plans for private repositories, and free accounts for open source projects. Large or small, every repository comes with the same powerful tools. These tools are open to the community for public projects and secure for private projects. Features include: * Integrated issue tracking * Collaborative code review * Easily manage teams within organizations * Text entry with understated power * A growing list of programming languages and data formats * On the desktop and in your pocket - Android app and mobile web views let you keep track of your projects on the go.

Proper citation: GitHub (RRID:SCR_002630) Copy   

•   Source: SciCrunch Registry

http://cucurbitgenomics.org/

Database to facilitate genomic and genetic data distribution, analysis, mining and integration for cucurbits. To store, mine, analyze, integrate and disseminate Cucurbitaceae family datasets and to provide central portal for cucurbit research and breeding community. Central portal for comparative and functional genomics of cucurbit crops.

Proper citation: CuGenDB (RRID:SCR_018401) Copy   

•   Source: SciCrunch Registry

https://github.com/lh3/minimap2

Software tool as pairwise alignment for nucleotide sequences. Alignment program to map DNA or long mRNA sequences against large reference database. Versatile pairwise aligner for genomic and spliced nucleotide sequences.

Proper citation: Minimap2 (RRID:SCR_018550) Copy   

•   Source: SciCrunch Registry

http://www.cgga.org.cn/

Web application for data storage and analysis to explore brain tumors datasets from Chinese cohorts. Data portal for storage and interactive exploration of multi-dimensional functional genomic data that includes primary and recurrent glioma samples from Chinese cohorts. Allows users to browse DNA mutation profile, mRNA/microRNA expression profile and methylation profile, and to do correlation and survival analysis in specific glioma subtype.

Proper citation: Chinese Glioma Genome Atlas (RRID:SCR_018802) Copy   

•   Source: SciCrunch Registry

http://enterobase.warwick.ac.uk/

Integrated software environment that supports identification of global population structures within several bacterial genera that include pathogens. Web service for analyzing and visualizing genomic variation within bacteria. Genome database to enable to identify, analyse, quantify and visualise genomic variation within bacterial genera including Salmonella, Escherichia/Shigella, Clostridioides,Vibrio,Yersinia,Helicobacter,Moraxella.

Proper citation: EnteroBase (RRID:SCR_019019) Copy   

•   Source: SciCrunch Registry

https://www.crd.york.ac.uk/PROSPERO

International database of prospectively registered systematic reviews in health and social care, welfare, public health, education, crime, justice, and international development, where there is health related outcome. Key features from review protocol are recorded and maintained as permanent record. Aims to provide comprehensive listing of systematic reviews registered at inception to help avoid duplication and reduce opportunity for reporting bias by enabling comparison of completed review with what was planned in protocol.

Proper citation: PROSPERO (RRID:SCR_019061) Copy   

•   Source: SciCrunch Registry