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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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European Mouse Phenotyping Resource of Standardised Screens Resource Report Resource Website 50+ mentions |
European Mouse Phenotyping Resource of Standardised Screens (RRID:SCR_003087) | EMPReSS | data or information resource, standard specification, narrative resource, data set | Database of validated Standard Operating Procedures (SOPs) for screens to determine the phenotype of a mouse, developed by the EUMORPHIA consortium. The SOP's cover all of the main body systems including: clinical chemistry, hormonal and metabolic systems, cardiovascular, allergy and infection, renal function, sensory function, neurological and behavioral function, cancer, bone and cartilage, and respiratory function. In addition, there are generic SOPs in histology, necropsy, pathology and gene expression. EMPReSS is a platform of individual tests. These can be performed as individual tests or grouped together in sequences, recommended in the EMPReSS database, to give more information on particular phenotype. Quick List of Current Pipelines: * EUMODIC Pipeline 1 * EUMODIC Pipeline 2 * GMC Pipeline * MGP Pipeline * Additional Tests * EUMODIC Pipeline 3 | phenotype, phenotyping, dysmorphology, body weight, blood pressure, calorimetry, ipgtt, dexa, x-ray, chemistry, clinical, heart weight, tibia length, standard operating procedure, FASEB list |
is related to: Understanding Human Disease Through Mouse Genetics is related to: Europhenome Mouse Phenotyping Resource is related to: Impress is related to: Europhenome Mouse Phenotyping Resource has parent organization: MRC Mammalian Genetics Unit |
PMID:17905814 | Free, Freely available | nif-0000-30492 | https://academic.oup.com/bioinformatics/article/21/12/2930/268092 | SCR_003087 | European Mouse Phenotyping Resource of Standardized Screens | 2026-08-15 11:22:25 | 78 | |||||
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Eukaryotic Linear Motif Resource Report Resource Website 100+ mentions |
Eukaryotic Linear Motif (RRID:SCR_003085) | ELM | database, production service resource, data analysis service, data or information resource, service resource, analysis service resource | Computational biology resource for investigating candidate functional sites in eukarytic proteins. Functional sites which fit to the description linear motif are currently specified as patterns using Regular Expression rules. To improve the predictive power, context-based rules and logical filters are being developed and applied to reduce the amount of false positives. The current version of the ELM server provides core functionality including filtering by cell compartment, phylogeny, globular domain clash (using the SMART/Pfam databases) and structure. In addition, both the known ELM instances and any positionally conserved matches in sequences similar to ELM instance sequences are identified and displayed (see ELM instance mapper). Although the ELM resource contains a large collection of functional site motifs, the current set of motifs is not exhaustive. | linear motif, regulatory protein, motif, protein sequence, functional site, prediction, disease, virus, cell compartment, phylogeny, globular domain clash, structure, protein, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is related to: SMART is related to: Pfam has parent organization: European Molecular Biology Laboratory |
EMBL international PhD program ; EMBL Interdisciplinary PostDoc fellowship ; Federal Government Department of Education and Science FKZ01GS0862; European Community Seventh Framework Programme FP7/2009 241955; European Community Seventh Framework Programme FP7/2009 242129; Polish Ministry of Science and Higher Education IP2010-0483-70; Biotechnology and Biological Sciences Research Council BB/F010486/1; Region Alsace and College Doctoral Europeen ; Science Foundation Ireland 08/IN.1/B1864; BBSRC BB/I006230/1; German Research Foundation SFB796; Swiss National Science Foundation |
PMID:22110040 | Free, Available for download, Freely available | biotools:elm, nif-0000-30486 | https://bio.tools/elm | SCR_003085 | Eukarotic Linear Motif resource for Functional Sites in Proteins | 2026-08-15 11:22:23 | 325 | ||||
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BioJS Resource Report Resource Website 10+ mentions |
BioJS (RRID:SCR_003119) | BioJS | software toolkit, data processing software, software application, software resource, data visualization software, software library | An open source JavaScript library of components for visualisation of biological data on the web. | javascript, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: The Genome Analysis Centre; Norwich; United Kingdom has parent organization: European Bioinformatics Institute |
BBSRC ; NHLBI HHSN268201000035C; European Union PSIMEx FP7-HEALTH-2007-223411 |
PMID:23435069 | Free, Freely available | biotools:biojs, nlx_156742 | http://www.ebi.ac.uk/Tools/biojs/registry/, https://bio.tools/biojs | http://www.tgac.ac.uk/tools-resources/biojs/ | SCR_003119 | 2026-08-15 11:22:26 | 22 | ||||
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Spider Ontology Resource Report Resource Website 1+ mentions |
Spider Ontology (RRID:SCR_003117) | SPD | ontology, data or information resource, controlled vocabulary | An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow). | obo, anatomy, organismal, behavior, product, spider |
is listed by: BioPortal is listed by: OBO has parent organization: Tree of Life: Phylogeny of Spiders |
Free, Freely available | nlx_157595 | http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/spider/spider_comparative_biology.obo | SCR_003117 | 2026-08-15 11:22:24 | 1 | |||||||
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bwtool Resource Report Resource Website 10+ mentions |
bwtool (RRID:SCR_003035) | software resource | A command-line utility for bigWig files designed to read bigWig files rapidly and efficiently, providing functionality for extracting data and summarizing it in several ways, globally or at specific regions. Its functionality is subdivided into subprograms that roughly fall into three categories: data extraction, analysis, and data modification, although e.g. in the case of the matrix program or the sax program, the boundary between data extraction and analysis isn't very strong. The data modification programs all have the behavior that a bigWig is inputted and a new bigWig is outputted. | standalone software, unix/linux, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:2448936 | Free, Available for download, Freely available | biotools:bwtool, OMICS_05125 | https://bio.tools/bwtool | SCR_003035 | 2026-08-15 11:22:23 | 22 | |||||||
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enviPat Resource Report Resource Website 10+ mentions |
enviPat (RRID:SCR_003034) | software resource | Software for fast and very memory-efficient calculation of isotope patterns, subsequent convolution to theoretical envelopes (profiles) plus valley detection and centroidization or intensoid calculation. Batch processing, resolution interpolation, wrapper, adduct calculations and molecular formula parsing. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
Free, Freely available | OMICS_02408 | SCR_003034 | enviPat: Isotope pattern profile and centroid calculation for mass spectrometry | 2026-08-15 11:22:24 | 33 | ||||||||
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Cytoscape Resource Report Resource Website 10000+ mentions |
Cytoscape (RRID:SCR_003032) | data processing software, software application, data analysis software, software resource, data visualization software | Software platform for complex network analysis and visualization. Used for visualization of molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. | biological, network, visualization, analysis, data, gene, pathway, molecular, interaction, FASEB list |
is used by: CytoSPADE is used by: HDBase is used by: DisGeNET is used by: categoryCompare lists: PEPPER is listed by: Debian is listed by: SoftCite is related to: PhosphoSitePlus: Protein Modification Site is related to: TRIP Database is related to: CoryneRegNet is related to: AltAnalyze - Alternative Splicing Analysis Tool is related to: MiMI Plugin for Cytoscape is related to: Network Data Exchange (NDEx) is related to: GeneMANIA is related to: DroID - Drosophila Interactions Database is related to: Network-based Prediction of Human Tissue-specific Metabolism is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: DaTo is related to: PiNGO is related to: iBIOFind is related to: cPath is related to: BiNGO: A Biological Networks Gene Ontology tool is related to: ClueGO is related to: RamiGO is related to: EGAN: Exploratory Gene Association Networks has parent organization: Institute for Systems Biology; Washington; USA has parent organization: University of California at San Diego; California; USA is parent organization of: JEPETTO has plug in: CluePedia Cytoscape plugin has plug in: CytoSPADE has plug in: EnrichmentMap has plug in: cytoHubba has plug in: iRegulon works with: NetCirChro works with: IMEx - The International Molecular Exchange Consortium works with: yFiles Layout Algorithms works with: RCy3 |
National Resource for Network Biology ; NCRR RR031228; NIGMS GM070743 |
PMID:21149340 PMID:14597658 |
Free, Available for download, Freely available | nif-0000-30404 | https://sources.debian.org/src/cytoscape/ | SCR_003032 | Complex Network Analysis Visualization, Cytoscape 2.6, Cytoscape 3.0 | 2026-08-15 11:22:22 | 25317 | |||||
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MoSDi Resource Report Resource Website 1+ mentions |
MoSDi (RRID:SCR_003037) | software toolkit, data processing software, software application, data analysis software, software resource | Sequence analysis toolkit that contains a lot of sequence analysis algorithms, including methods for 1) motif statistics, e.g. compute the exact occurrence count distribution of a motif, 2) exact motif discovery: extraction of motifs with provably optimal p-value, 3) analysis of pattern matching algorithms: compute (for given algorithm and pattern) the exact distribution of the number of character accesses caused by searching a random text, 4) statistics of fragment masses resulting from proteolytic cleavage of proteins, 5) computing the expectated read length of sequencing reads for a given dispensation order (for 454 or IonTorrent) and 6) analysing sensitivity of spaced alignment seeds. | standalone software, unix/linux, motif |
is listed by: OMICtools has parent organization: Google Code |
PMID:19478010 | Free, Freely available | OMICS_06271 | https://bio.tools/mosdi | SCR_003037 | Motif Statistics and Discovery, Motif Statistics and Discovery - Sequence analysis toolkit for bioinformatics | 2026-08-15 11:22:24 | 2 | ||||||
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DGAP Resource Report Resource Website 1+ mentions |
DGAP (RRID:SCR_003036) | DGAP | database, experimental protocol, data or information resource, resource, narrative resource | Produce resources to unravel the interface between insulin action, insulin resistance and the genetics of type 2 diabetes including an annotated public database, standardized protocols for gene expression and proteomic analysis, and ultimately diabetes-specific and insulin action-specific DNA chips for investigators in the field. The project aims to identify the sets of the genes involved in insulin action and the predisposition to type 2 diabetes, as well as the secondary changes in gene expression that occur in response to the metabolic abnormalities present in diabetes. There are five major and one pilot project involving human and rodent tissues that are designed to: * Create a database of the genes expressed in insulin-responsive tissues, as well as accessible tissues, that are regulated by insulin, insulin resistance and diabetes. * Assess levels and patterns of gene expression in each tissue before and after insulin stimulation in normal and genetically-modified rodents; normal, insulin resistant and diabetic humans, and in cultured and freshly isolated cell models. * Correlate the level and patterns of expression at the mRNA and/or protein level with the genetic and metabolic phenotype of the animal or cell. * Generate genomic sequence from a panel of humans with type 2 diabetes focusing on the genes most highly regulated by insulin and diabetes to determine the range of sequence and expression variation in these genes and the proteins they encode, which might affect the risk of diabetes or insulin resistance. The DGAP project will define: * the normal anatomy of gene expression, i.e. basal levels of expression and response to insulin. * the morbid anatomy of gene expression, i.e., the impact of diabetes on expression patterns and the insulin response. * the extent to which genetic variability might contribute to the alterations in expression or to diabetes itself. | gene, insulin action, predisposition, gene expression, metabolic abnormality, diabetes, insulin resistance, genetics, insulin, genetic variation, proteomics, genomics, affymetrix oligonucleotide array, microarray, protein, genomic sequence, data set |
is related to: NIDDK Information Network (dkNET) has parent organization: Harvard Medical School; Massachusetts; USA has parent organization: Broad Institute has parent organization: Dana-Farber Cancer Institute has parent organization: University of Massachusetts Medical School; Massachusetts; USA has parent organization: University of Southern Denmark; Odense; Denmark |
Type 2 diabetes, Normal, Insulin resistance | NIDDK | PMID:19786482 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30414 | SCR_003036 | The Diabetes Genome Anatomy Project, Diabetes Genome Anatomy Project | 2026-08-15 11:22:22 | 9 | ||||
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JASPAR Resource Report Resource Website 5000+ mentions |
JASPAR (RRID:SCR_003030) | JASPAR | database, production service resource, data analysis service, data or information resource, service resource, analysis service resource | Open source database of curated, non-redundant set of profiles derived from published collections of experimentally defined transcription factor binding sites for multicellular eukaryotes. Consists of open data access, non-redundancy and quality. JASPAR CORE is smaller set that is non-redundant and curated. Collection of transcription factor DNA-binding preferences, modeled as matrices. These can be converted into Position Weight Matrices (PWMs or PSSMs), used for scanning genomic sequences. Web interface for browsing, searching and subset selection, online sequence analysis utility and suite of programming tools for genome-wide and comparative genomic analysis of regulatory regions. New functions include clustering of matrix models by similarity, generation of random matrices by sampling from selected sets of existing models and a language-independent Web Service applications programming interface for matrix retrieval. | structural class, transcription factor binding site, profile, regulatory region, genome, genomic, matrix, transcription factor, binding site, dna, FASEB list |
is listed by: OMICtools is listed by: re3data.org is related to: Babelomics has parent organization: University of Copenhagen; Copenhagen; Denmark has parent organization: Karolinska Institute; Stockholm; Sweden |
Novo Nordisk Foundation ; European Union ; EMBRACEa Sixth Framework Network of Excellence ; Sars Centre ; Carlsberg Foundation |
PMID:18006571 PMID:16381983 PMID:14681366 |
Free, Freely available | r3d100010091, OMICS_00538, nif-0000-03061 | https://doi.org/10.17616/R3QC7R | http://129.177.120.189/cgi-bin/jaspar2010/jaspar_db.pl, http://jaspar.cgb.ki.se | SCR_003030 | JASPAR, JASPAR CORE, JASPAR CORE database, JASPAR database | 2026-08-15 11:22:23 | 5785 | |||
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Gel2DE Resource Report Resource Website 1+ mentions |
Gel2DE (RRID:SCR_002977) | software resource | Software application for performing pixel-by-pixel correlation analysis on a set of gel images from two-dimensional gel electrophoresis and a set of clinical parameters for a population. The application is written in C++, and has been tested on Windows, although it in principle should compile cross platform using CMake. | windows, c++, correlation analysis, gel electrophoresis |
is listed by: OMICtools has parent organization: Google Code |
PMID:23829206 | Free, Available for download, Freely available | OMICS_02546 | SCR_002977 | gel2de - Correlation analysis of gel electrophoresis data | 2026-08-15 11:22:22 | 2 | |||||||
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ChIPMonk Resource Report Resource Website 1+ mentions |
ChIPMonk (RRID:SCR_002975) | ChIPMonk | software resource | Software tool to visualize and analyse ChIP-on-chip array data. Main features: * Import of data from Nimblegen arrays (other formats can be added if people send us examples) * Normalization of data (both per array and per probe) * Various data plotting options to assess data quality and the effectiveness of normalization * Creation of data groups for visualization and analysis * Visualization of data against an annotated genome. * Statistical analysis of data to find probes of interest * Creation of reports containing probes, data and genome annotation Note: This project is no longer being developed, but critical bug fixes will still be provided | java, chip, chip-on-chip, plotting, normalization, visualization, genome, annotation, probe, array, analysis |
is listed by: OMICtools has parent organization: Babraham Institute |
Free, Available for download, Freely available | OMICS_02043, nif-0000-30159 | http://www.bioinformatics.bbsrc.ac.uk/projects/chipmonk/ | SCR_002975 | 2026-08-15 11:22:23 | 4 | |||||||
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ms lims Resource Report Resource Website 1+ mentions |
ms lims (RRID:SCR_002974) | software application, software resource, data management software | Software that provides a lightweight, portable yet production-grade solution for managing mass spectrometry based proteomics data. | mass spectrometry, proteomics, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Google Code |
PMID:20058248 | Free, Available for download, Freely available | OMICS_02547, biotools:ms-lims | https://bio.tools/ms-lims | SCR_002974 | mass spectrometry based proteomics information management system, ms-lims: mass spectrometry based proteomics information management system | 2026-08-15 11:22:21 | 1 | ||||||
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SMRT View Resource Report Resource Website 1+ mentions |
SMRT View (RRID:SCR_003029) | software resource | An open source Genome Browser that visualizes data generated by PacBio Sequencing Systems. * Users can explore and interact with all types of analysis results, including resequencing, De novo, cDNA, and barcoding. * Users can also visualize base modifications, base identification and motifs analysis results. | standalone software, unix/linux, mac os x, windows, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:smrt_view, OMICS_05137 | https://bio.tools/smrt_view | SCR_003029 | SMRT-View | 2026-08-15 11:22:24 | 9 | |||||||
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EONS Resource Report Resource Website 10+ mentions |
EONS (RRID:SCR_002979) | EONS | software application, simulation software, software resource | Modeling platform to study the basic interactions between synaptic elements that allows the user to study qualitatively, and also quantitatively the relative contributions of diverse mechanisms underlying synaptic efficacy: the relevance of each and every element that comprises a synapse, the interactions between these components and their subcellular distribution, as well as the influence of synaptic geometry (presynaptic terminal, cleft and postsynaptic density). This platform consists of a graphical interface in which elements that comprise a single glutamatergic synapse (both pre- and post-synaptically), their behavior as well as the underlying synaptic geometry can be modified. For example, EONS offers the ability to study the effect of voltage-gated calcium channels density and distribution, the number and location of receptors and more. EONS is a parametric model of a generic glutamatergic synapse that takes into account pre-synaptic mechanisms, such as calcium buffering and diffusion, neurotransmitter release, diffusion and uptake in the cleft, and postsynaptic elements, such as ionotropic AMPA and NMDA receptors, their distribution and synaptic geometry, as well as metabotropic glutamate receptors. There are no complicated equations to write: all the models are predefined. This version is a great tool for first time users and students interested in learning about synapses, as well as for studying geometry and distribution hypotheses in a 2D rectangular geometry. System Requirements: EONS V1.2 is a Windows program but can be also successfully installed and run on Mac and Linux. | synapse, geometry, distribution hypothesis, 2d, synaptic modeling, synaptic, modeling, neuron, nervous system, presynaptic, postsynaptic, electromicrograph, animation, simulation, calcium channel, synaptic cleft, excitatory postsynaptic potential, potassium channel, computational neuroscience, java, macos, microsoft, windows, windows xp |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Biomedical Simulations Resource |
NIBIB P41-EB001978 | PMID:17946227 | Free, Available for download, Freely available | nif-0000-00504 | http://www.nitrc.org/projects/eons, http://synapticmodeling.com/ | http://www.synaptic-modeling.com | SCR_002979 | Elementary Objects of the Nervous System, EONS-The integrated synaptic modeling platform, EONS (Elementary Objects of the Nervous System) | 2026-08-15 11:22:21 | 12 | |||
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BMAP cDNA Resources Resource Report Resource Website 1+ mentions |
BMAP cDNA Resources (RRID:SCR_002973) | BMAP Resources | topical portal, production service resource, portal, biomaterial manufacture, data or information resource, resource, material service resource, service resource | As part of BMAP gene discovery efforts, mouse brain cDNA libraries and Expressed Sequence Tags (ESTs) have been generated. Through this project a BMAP mouse brain UniGene set consisting of over 24,000 non-redundant members of unique clusters has been developed from EST sequencing of more than 50,000 cDNA clones from 10 regions of adult mouse brain, spinal cord, and retina (http://brainEST.eng.uiowa.edu/). In 2001, NIMH along with NICHD, NIDDK, and NIDA, awarded a contract to the University of Iowa ( M.B. Soares, PI) to isolate full-length cDNA clones corresponding to genes expressed in the developing mouse nervous system and determine their full-coding sequences. The BMAP mouse brain EST sequences can be accessed at NCBI's dbEST database (http://www.ncbi.nlm.nih.gov/dbEST/). Arrayed sets of BMAP mouse brain UniGenes and cDNA libraries, and individual BMAP cDNA clones can be purchased from Open Biosystems, Huntsville, AL (http://www.openbiosystems.com | brain, spinal cord, retina, gene, cdna, library, est, cluster, clone, nervous system, dbest, database, gene discovery, cdna library, expressed sequence tag, coding sequence, adult |
is related to: Nucleotide database is related to: Open Biosystems has parent organization: BMAP - Brain Molecular Anatomy Project |
NINDS ; NICHD ; NIDDK ; NIDA ; NIMH N01 MH80014 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30154 | SCR_002973 | Brain Molecular Anatomy Project cDNA Resources | 2026-08-15 11:22:22 | 2 | ||||||
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pbh5tools Resource Report Resource Website 10+ mentions |
pbh5tools (RRID:SCR_003027) | software resource | Software tools for manipulating HDF5 files produced by Pacific Biosciences. Specifically, this package provides functionality for manipulating and extracting data from cmp.h5 and bas.h5 files. | standalone software | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_05138 | http://132.248.34.22:8080/smrtanalysis/doc/bioinformatics-tools/pbh5tools/doc/index.html | SCR_003027 | 2026-08-15 11:22:22 | 10 | ||||||||
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IMGT/HLA Resource Report Resource Website 100+ mentions |
IMGT/HLA (RRID:SCR_002971) | IMGT HLA, IMGT/HLA | database, data repository, storage service resource, data or information resource, service resource | Database for sequences of the human major histocompatibility complex (HLA) and includes the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. It currently contains 9,310 allele sequences (2013) along with detailed information concerning the material from which the sequence was derived and data on the validation of the sequences. It is established procedure for authors to submit the sequences directly to the IMGT/HLA Database for checking and assignment of an official name prior to publication, this avoids the problems associated with renaming published sequences and the confusion of multiple names for the same sequence. The need for reasonably rapid publication of new HLA allele sequences has necessitated an annual meeting of the WHO Nomenclature Committee for Factors of the HLA System. Additionally they now publish monthly HLA nomenclature updates both in journals and online to provide quick and easy access to new sequence information. The IMGT/HLA Database is part of the international ImMunoGeneTics project. In collaboration with the Imperial Cancer Research Fund (ICRF) and European Bioinformatics Institute (EBI) they have developed an Oracle database to house the HLA sequences in such a way as to allow users to present complex queries about the sequence, sequence features, references, contacts and allele designations to the database via a graphical user interface over the web. The IMGT/HLA Database Submission Tool allows direct submission of sequences to the WHO HLA Nomenclature Committee for Factors of the HLA System. The IMGT/HLA Database provides an FTP site for the retrieval of sequences in a number of pre-formatted files. | alignment, allele, cell, hla, sequence alignment, major histocompatibility complex, nomenclature, blast, immunogenetics, histocompatibility, gene mapping, gene rearrangement, genetic recombination, genetics, gold standard, bio.tools |
is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: dbMHC has parent organization: European Bioinformatics Institute has parent organization: Anthony Nolan Research Institute has parent organization: IMGT - the international ImMunoGeneTics information system |
EU Biotech grant BIO4CT960037; Anthony Nolan Trust ; Imperial Cancer Research Fund |
PMID:21071412 PMID:10777106 PMID:18838392 |
Creative Commons Attribution-NoDerivs License | nif-0000-03014, biotools:ipd-imgt_hla, r3d100010804 | https://bio.tools/ipd-imgt_hla, https://doi.org/10.17616/R3T31N | SCR_002971 | IMGT HLA, IMGT/HLA DB, IMGT/HLA Database, International ImMunoGeneTics/Human Leukocyte Antigen Database | 2026-08-15 11:22:23 | 291 | ||||
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ISFinder Resource Report Resource Website 1000+ mentions |
ISFinder (RRID:SCR_003020) | ISFinder | database, data repository, production service resource, storage service resource, data analysis service, data or information resource, service resource, analysis service resource | Database of a list of insertion sequences isolated from eubacteria and archaea. It is organized into individual files containing their general features (name, size, origin, family.....) as well as their DNA and potential protein sequences. Although most of the entries have been identified as individual elements, a growing number are included from their description in sequenced bacterial genomes. The search engine permits the retrieval and display of individual and groups of ISs based on a combination of their general features. Two levels of search are available. The simple search option enables the user to sort elements using a limited number of basic items whereas the extensive search offers an additional set of possibilities such as comparisons of the sequences of terminal inverted repeats and a variety of different layout displays. Built in links are provided to: the EMBL sequence database, the NCBI taxonomy database and to the ESF plasmid database. At present, only individual sequences can be downloaded one by one for comparison. An on-line BLAST facility is available and in future versions direct access to additional analytical tools will be provided on line. Direct submission of ISs is encouraged using the on-line form provided. | insertion sequence, insertion, sequence, blast, dna, protein sequence, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: Paul Sabatier University - Toulouse III; Toulouse; France |
CNRS | PMID:22367867 PMID:19906702 |
biotools:isfinder, nif-0000-03050 | https://bio.tools/isfinder | SCR_003020 | IS Finder, Isfinder | 2026-08-15 11:22:24 | 1181 | |||||
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CompuCell3D Resource Report Resource Website 50+ mentions |
CompuCell3D (RRID:SCR_003052) | CC3D | software application, simulation software, software resource | Open-source simulation environment for multi-cell, single-cell-based modeling of tissues, organs and organisms. It uses Cellular Potts Model to model cell behavior. | model, simulation, cellular, multi-cellular, windows, mac os x, linux, tissue, organ, organism, cell behavior | has parent organization: Indiana University; Indiana; USA | NIH ; EPA |
PMID:22482955 | Free, Available for download, Freely available | nlx_157668 | SCR_003052 | 2026-08-15 11:22:25 | 75 |
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