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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MicrobesOnline Resource Report Resource Website 100+ mentions |
MicrobesOnline (RRID:SCR_005507) | MicrobesOnline | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource, software resource, source code | MicrobesOnline is designed specifically to facilitate comparative studies on prokaryotic genomes. It is an entry point for operon, regulons, cis-regulatory and network predictions based on comparative analysis of genomes. The portal includes over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms ranging from model organisms such as Escherichia coli and Saccharomyces cerevisiae to environmental microbes such as Desulfovibrio vulgaris and Shewanella oneidensis. To assist in annotating genes and in reconstructing their evolutionary history, MicrobesOnline includes a comparative genome browser based on phylogenetic trees for every gene family as well as a species tree. To identify co-regulated genes, MicrobesOnline can search for genes based on their expression profile, and provides tools for identifying regulatory motifs and seeing if they are conserved. MicrobesOnline also includes fast phylogenetic profile searches, comparative views of metabolic pathways, operon predictions, a workbench for sequence analysis and integration with RegTransBase and other microbial genome resources. The next update of MicrobesOnline will contain significant new functionality, including comparative analysis of metagenomic sequence data. Programmatic access to the database, along with source code and documentation, is available at http://microbesonline.org/programmers.html. | microbe, genome, bacteria, archaea, fungi, prokaryote, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: Lawrence Berkeley National Laboratory |
DOE DE-AC02-05CH11231 | PMID:19906701 | nlx_144607, biotools:microbesonline | https://bio.tools/microbesonline | SCR_005507 | Microbial Genomics Database, Microbes Online | 2026-09-12 12:56:27 | 166 | |||||
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DiProGB Resource Report Resource Website 1+ mentions |
DiProGB (RRID:SCR_005651) | DiProGB | software resource | Genome browser that encodes the genome sequence by physico-chemical dinucleotide properties such as stacking energy, melting temperature or twist angle. Analyses can be performed for the + and ?, as well as for the double strand. | genome, browser, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Dinucleotide Property Database |
PMID:19605418 | Free, Freely available | biotools:diprogb, OMICS_00880 | https://bio.tools/diprogb | SCR_005651 | DiProGB - The Dinucleotide Properties Genome Browser, Dinucleotide Properties Genome Browser | 2026-09-12 12:56:29 | 4 | |||||
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Bambino Resource Report Resource Website 1+ mentions |
Bambino (RRID:SCR_005649) | Bambino | analysis service resource, data analysis service, production service resource, service resource, software resource | A variant detector and graphical alignment viewer for next-generation sequencing data in the SAM/BAM format, which is capable of pooling data from multiple source files. Bambino may be launched online via Java Web Start or downloaded and run locally. | java, next-generation sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: National Cancer Institute |
PMID:21278191 | Https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/Bambino_Click-thru-agreement-for-executable_final.txt | OMICS_00876, biotools:bambino | https://bio.tools/bambino | SCR_005649 | Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format | 2026-09-12 12:56:29 | 5 | |||||
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BS Seeker Resource Report Resource Website 1+ mentions |
BS Seeker (RRID:SCR_005641) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software which performs accurate and fast mapping of bisulfite-treated short reads. Supplementary information and examples are provided on the site. | bisulfite sequencing, sequence analysis software, short read, sequence mapping, bio.tools |
uses: Bowtie is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Bs-Seeker2 has parent organization: University of California at Los Angeles; California; USA |
PMID:20416082 | Free, Available for download, Freely available | OMICS_00578, biotools:bs_seeker | https://bio.tools/bs_seeker | SCR_005641 | Bisulfite Sequence Seeker | 2026-09-12 12:56:29 | 3 | ||||||
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DMRforPairs Resource Report Resource Website 1+ mentions |
DMRforPairs (RRID:SCR_005702) | software resource | Software for identifying differentially methylated regions between unique samples using array based methylation profiles. It allows researchers to compare n greater than or equal to 2 unique samples with regard to their methylation profile. The (pairwise) comparison of n unique single samples distinguishesit from other existing pipelines as these often compare groups of samples in either single CpG locus or region based analysis. DMRforPairs defines regions of interest as genomic ranges with sufficient probes located in close proximity to each other. Probes in one region are optionally annotated to the same functional class(es). Differential methylation is evaluated by comparing the methylation values within each region between individual samples and (if the difference is sufficiently large), testing this difference formally for statistical significance. | standalone software, mac os x, unix/linux, windows, r, annotation, dna methylation, differential methylation, microarray, report writing, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:24884391 | GNU General Public License, v2 or greater | biotools:dmrforpairs, OMICS_04059 | https://bio.tools/dmrforpairs | SCR_005702 | DMR2+, DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles | 2026-09-12 12:56:30 | 4 | ||||||
|
Bismark Resource Report Resource Website 1000+ mentions |
Bismark (RRID:SCR_005604) | Bismark | software resource | Software tool to map bisulfite converted sequence reads and determine cytosine methylation states. Flexible aligner and methylation caller for Bisulfite-Seq applications. Used to map bisulfite treated sequencing reads to genome of interest and perform methylation calls in single step. | Map bisulfite treated sequence reads, determine cytosine methylation states, genome, sequence reads, perform methylation calls, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Babraham Institute |
PMID:21493656 DOI:10.1093/bioinformatics/btr167 |
Free, Available for download, Freely available | biotools:bismark, OMICS_00575 | https://github.com/FelixKrueger/Bismark, https://bio.tools/bismark | https://sources.debian.org/src/bismark/ | SCR_005604 | 2026-09-12 12:56:28 | 1200 | |||||
|
ToppGene Suite Resource Report Resource Website 1000+ mentions |
ToppGene Suite (RRID:SCR_005726) | analysis service resource, data analysis service, data or information resource, database, portal, production service resource, resource, service resource | ToppGene Suite is a one-stop portal for gene list enrichment analysis and candidate gene prioritization based on functional annotations and protein interactions network. ToppGene Suite is a one-stop portal for (i) gene list functional enrichment, (ii) candidate gene prioritization using either functional annotations or network analysis and (iii) identification and prioritization of novel disease candidate genes in the interactome. Functional annotation-based disease candidate gene prioritization uses a fuzzy-based similarity measure to compute the similarity between any two genes based on semantic annotations. The similarity scores from individual features are combined into an overall score using statistical meta-analysis. | gene portal, enrichment analysis, functional annotation, gene prioritization, protein interaction, bio.tools, FASEB list |
is listed by: Gene Ontology Tools is listed by: NIDDK Information Network (dkNET) is listed by: GUDMAP Ontology is listed by: Debian is listed by: bio.tools is related to: Gene Ontology is related to: ToppCluster |
State of Ohio Computational Medicine Center ODD TECH 04-042; NIDDK 1U01DK70219; NIDDK P30DK078392 |
PMID:19465376 | Free for academic use | nlx_149183, biotools:toppgene_suite | https://bio.tools/toppgene_suite | SCR_005726 | ToppGene | 2026-09-12 12:56:30 | 1131 | |||||
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TMAJ Resource Report Resource Website 10+ mentions |
TMAJ (RRID:SCR_005601) | TMAJ | software resource | Open-source software to support information and images related to tissue micro-arrays. It contains support for multiple organ systems, multiple users, image analysis, and is designed to be compliant with HIPPA regulations. Patients, specimens, blocks, slides, cores, images, and scores can all be stored and viewed. Features include advanced security, custom dynamic fields, and an image analysis program. | tissue microarray, java, java swing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Johns Hopkins University; Maryland; USA has parent organization: SourceForge |
GNU General Public License, v3 | biotools:tmaj, OMICS_00823 | https://bio.tools/tmaj | SCR_005601 | TMAJ Software Project | 2026-09-12 12:56:28 | 10 | ||||||
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GoFish Resource Report Resource Website 1+ mentions |
GoFish (RRID:SCR_005682) | GoFish | analysis service resource, data analysis service, production service resource, service resource, software resource, source code | Software program, available as a Java applet online or to download, allows the user to select a subset of Gene Ontology (GO) attributes, and ranks genes according to the probability of having all those attributes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, ontology or annotation browser, java, windows, mac os x, linux, unix, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: University of Toronto; Ontario; Canada has parent organization: Harvard Medical School; Massachusetts; USA |
Aventis Pharmaceuticals ; Howard Hughes Medical Institute ; NHGRI |
PMID:12691998 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:gofish, nlx_149126, OMICS_02272 | http://llama.mshri.on.ca/Software.html, https://bio.tools/gofish | SCR_005682 | 2026-09-12 12:56:29 | 1 | |||||
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Maqview Resource Report Resource Website |
Maqview (RRID:SCR_005632) | MaqView | data processing software, data visualization software, software application, software resource | A graphical read alignment viewer specifically designed for the Maq alignment file and allows you to see the mismatches, base qualities and mapping qualities. It is highly efficient in speed, memory and disk usage. Maqview is based on OpenGL and is known to work on both Mac OS X and Linux. Porting to Windows is in principle easy. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
DOI:10.1101/gr.078212.108 | GNU General Public License | OMICS_00889, biotools:maqview | https://bio.tools/maqview, https://sources.debian.org/src/maqview/ | SCR_005632 | Mapping and Assembly with Qualities Viewer, M.A.Q Viewer | 2026-09-12 12:56:29 | 0 | |||||
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Staden Package Resource Report Resource Website 50+ mentions |
Staden Package (RRID:SCR_005629) | software resource | A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows. | c, unix/linux, sequence assembly, dna/protein analysis, spin, sequence alignment, genome, genome viewer, c++, fortran, tcl, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:20513662 DOI:10.1093/bioinformatics/btq268 |
BSD License | OMICS_00894, biotools:staden | https://bio.tools/staden, https://sources.debian.org/src/staden/ | SCR_005629 | Staden Package | 2026-09-12 12:56:29 | 87 | ||||||
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FunCluster Resource Report Resource Website 1+ mentions |
FunCluster (RRID:SCR_005774) | FunCluster | data analysis software, data processing software, software application, software resource | FunCluster is a genomic data analysis algorithm which performs functional analysis of gene expression data obtained from cDNA microarray experiments. Besides automated functional annotation of gene expression data, FunCluster functional analysis aims to detect co-regulated biological processes through a specially designed clustering procedure involving biological annotations and gene expression data. FunCluster''''s functional analysis relies on Gene Ontology and KEGG annotations and is currently available for three organisms: Homo Sapiens, Mus Musculus and Saccharomyces Cerevisiae. FunCluster is provided as a standalone R package, which can be run on any operating system for which an R environment implementation is available (Windows, Mac OS, various flavors of Linux and Unix). Download it from the FunCluster website, or from the worldwide mirrors of CRAN. FunCluster is provided freely under the GNU General Public License 2.0. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | genomic, gene, functional analysis, gene expression, cdna microarray, cdna, microarray, function, cluster, annotation, biological process, statistical analysis, bio.tools |
is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology has parent organization: Cordelier Research Center |
PMID:17007070 PMID:16506959 PMID:16046292 |
Free for academic use, GNU General Public License, v2 | nlx_149242, biotools:funcluster | https://bio.tools/funcluster | SCR_005774 | FunCluster R Package, FunCluster Algorithm | 2026-09-12 12:56:31 | 2 | |||||
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InterProScan Resource Report Resource Website 5000+ mentions |
InterProScan (RRID:SCR_005829) | analysis service resource, data access protocol, data analysis service, data analysis software, data processing software, production service resource, service resource, software application, software resource, web service | Software package for functional analysis of sequences by classifying them into families and predicting presence of domains and sites. Scans sequences against InterPro's signatures. Characterizes nucleotide or protein function by matching it with models from several different databases. Used in large scale analysis of whole proteomes, genomes and metagenomes. Available as Web based version and standalone Perl version and SOAP Web Service. | functional, analysis, sequence, protein, nucleotide, predict, presence, domain, site, proteome, genome, metagenome, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Gene Ontology is related to: RARTF is related to: InterPro is related to: LegumeIP is related to: UniProtKB has parent organization: European Bioinformatics Institute |
Biotechnology and Biological Sciences Research Council ; EMBL ; European Union |
PMID:15980438 PMID:17202162 PMID:24451626 |
Free, Available for download, Freely available | OMICS_01479, biotools:interproscan_4, nlx_149337 | https://www.ebi.ac.uk/interpro/download.html, https://bio.tools/interproscan_4 | SCR_005829 | InterProScan Sequence Search, InterProScan 2, InterProScan 3, InterProScan 4, InterProScan 5 | 2026-09-12 12:56:32 | 7512 | |||||
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ccPDB - Compilation and Creation of datasets from PDB Resource Report Resource Website 1+ mentions |
ccPDB - Compilation and Creation of datasets from PDB (RRID:SCR_005870) | ccPDB | data access protocol, data or information resource, database, software resource, web service | ccPDB (Compilation and Creation of datasets from PDB) is designed to provide service to scientific community working in the field of function or structure annoation of proteins. This database of datasets is based on Protein Data Bank (PDB), where all datasets were derived from PDB. ccPDB have four modules; i) compilation of datasets, ii) creation of datasets, iii) web services and iv) Important links. * Compilation of Datasets: Datasets at ccPDB can be classified in two categories, i) datasets collected from literature and ii) datasets compiled from PDB. We are in process of collecting PDB datasetsfrom literature and maintaining at ccPDB. We are also requesting community to suggest datasets. In addition, we generate datasets from PDB, these datasets were generated using commonly used standard protocols like non-redundant chains, structures solved at high resolution. * Creation of datasets: This module developed for creating customized datasets where user can create a dataset using his/her conditions from PDB. This module will be useful for those users who wish to create a new dataset as per ones requirement. This module have six steps, which are described in help page. * Web Services: We integrated following web services in ccPDB; i) Analyze of PDB ID service allows user to submit their PDB on around 40 servers from single point, ii) BLAST search allows user to perform BLAST search of their protein against PDB, iii) Structural information service is designed for annotating a protein structure from PDB ID, iv) Search in PDB facilitate user in searching structures in PDB, v)Generate patterns service facility to generate different types of patterns required for machine learning techniques and vi) Download useful information allows user to download various types of information for a given set of proteins (PDB IDs). * Important Links: One of major objectives of this web site is to provide links to web servers related to functional annotation of proteins. In first phase we have collected and compiled these links in different categories. In future attempt will be made to collect as many links as possible. | secondary structure, nucleic acid interaction, ligand interaction, structure, nucleic acid, interaction, ligand, data set, function, protein, annotate, tight-turn, nucleotide interacting residue, metals interacting residue, dna/rna binding residue, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: Institute of Microbial Technology; Chandigarh; India |
OSDD ; DBT ; Council of Scientific and Industrial Research; New Delhi; India |
PMID:22139939 | biotools:ccpdb, nlx_149416 | https://bio.tools/ccpdb | SCR_005870 | Compilation and Creation of datasets from PDB, ccPDB - Compilation Creation of datasets from PDB | 2026-09-12 12:56:32 | 2 | |||||
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UTRdb/UTRsite Resource Report Resource Website 10+ mentions |
UTRdb/UTRsite (RRID:SCR_005868) | data or information resource, portal, topical portal | UTRdb/UTRsite is a portal to other databases, including Nucleotide Sequence Databases, Protein Sequence Databases, other Sequence databanks, Untranslated Nucleotide Sequence Databases, Mitochondrial Databases, Mutation Databases, and others. The site also allows users to start long-term permanent projects or just to do quick searches, depending on the user''s needs. | bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian |
biotools:utrdb, nif-0000-03619 | https://bio.tools/utrdb | http://bighost.area.ba.cnr.it/srs6/ | SCR_005868 | UTRdb/UTRsite | 2026-09-12 12:56:32 | 41 | |||||||
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DiseaseMeth Resource Report Resource Website 10+ mentions |
DiseaseMeth (RRID:SCR_005942) | data or information resource, data repository, database, service resource, storage service resource | Human disease methylation database. DiseaseMeth version 2.0 is focused on aberrant methylomes of human diseases. Used for understanding of DNA methylation driven human diseases. | disease, methylation, dna methylation, genome, gene, epigenetics, epigenomics, methylome, bio.tools |
is listed by: 3DVC is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Harbin Medical University; Heilongjiang; China |
National Natural Science Foundation of China ; Natural Science Foundation of Heilongjiang Province ; Scientific Research Fund of Heilongjiang Provincial Education Department ; State Key Laboratory of Urban Water Resource and Environment |
PMID:22135302 PMID:27899673 |
Free,Freely available | OMICS_01838, nlx_151289, biotools:diseasemeth, SCR_017488 | http://bioinfo.hrbmu.edu.cn/diseasemeth, https://bio.tools/diseasemeth | http://202.97.205.78/diseasemeth/ | SCR_005942 | , Disease Meth-The Human Disease Methylation Database, DiseaseMeth database, DiseaseMeth version 2.0 | 2026-09-12 12:56:33 | 44 | ||||
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DistiLD - Diseases and Traits in LD Resource Report Resource Website 1+ mentions |
DistiLD - Diseases and Traits in LD (RRID:SCR_005943) | DistiLD | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | The DistiLD database aims to increase the usage of existing genome-wide association studies (GWAS) results by making it easy to query and visualize disease-associated SNPs and genes in their chromosomal context. The database performs three important tasks: # published GWAS are collected from several sources and linked to standardized, international disease codes ICD10 codes) # data from the International HapMap Project are analyzed to define linkage disequilibrium (LD) blocks onto which SNPs and genes are mapped # the web interface makes it easy to query and visualize disease-associated SNPs and genes within LD blocks. Users can query the database by diseases, SNPs or genes. No matter which of the three query modes was used, an intermediate page will be shown listing all the studies that matched the search with a link to the corresponding publication. The user can select either all studies related to a certain disease or one specific study for which to view the related LD blocks. The DistiLD resource integrates information on: * Associations between Single Nucleotide Polymorphisms (SNPs) and diseases from genome-wide association studies (GWAS) * Links between SNPs and genes based on linkage disequilibrium (LD) data from HapMap For convenience, we provide the complete datasets as two (zipped) tab-delimited files. The first file contains GWAS results mapped to LD blocks. The second file contains all SNPs and genes assigned to each LD block. | disease, mutation, gene, linkage disequilibrium, trait, genome-wide association study, single nucleotide polymorphism, chromosomal region, chromosome, linkage disequilibrium block, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: International HapMap Project has parent organization: University of Copenhagen; Copenhagen; Denmark |
Novo Nordisk Foundation Center for Protein Research | PMID:22058129 | Files are published under the Creative Commons Attribution v3 License | biotools:distild, nlx_151291 | https://bio.tools/distild | SCR_005943 | DistiLD - Diseases & Traits in LD, Diseases and Traits In Linkage Disequilibrium blocks, Diseases and Traits In Linkage Disequilibrium, DistiLD Database, DistiLD - Diseases Traits in LD | 2026-09-12 12:56:33 | 5 | ||||
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Newtomics Resource Report Resource Website 1+ mentions |
Newtomics (RRID:SCR_006073) | Newt-Omics | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Newt-omics is a database, which enables researchers to locate, retrieve and store data sets dedicated to the molecular characterization of newts. Newt-omics is a transcript-centered database, based on an Expressed Sequence Tag (EST) data set from the newt, covering ~50,000 Sanger sequenced transcripts and a set of high-density microarray data, generated from regenerating hearts. Newt-omics also contains a large set of peptides identified by mass spectrometry, which was used to validate 13,810 ESTs as true protein coding. Newt-omics is open to implement additional high-throughput data sets without changing the database structure. Via a user-friendly interface Newt-omics allows access to a huge set of molecular data without the need for prior bioinformatical expertise. The newt Notopthalmus viridescens is the master of regeneration. This organism is known for more than 200 years for its exceptional regenerative capabilities. Newts can completely replace lost appendages like limb and tail, lens and retina and parts of the central nervous system. Moreover, after cardiac injury newts can rebuild the functional myocardium with no scar formation. To date only very limited information from public databases is available. Newt-Omics aims to provide a comprehensive platform of expressed genes during tissue regeneration, including extensive annotations, expression data and experimentally verified peptide sequences with yet no homology to other publicly available gene sequences. The goal is to obtain a detailed understanding of the molecular processes underlying tissue regeneration in the newt, that may lead to the development of approaches, efficiently stimulating regenerative pathways in mammalians. * Number of contigs: 26594 * Number of est in contigs: 48537 * Number of transcripts with verified peptide: 5291 * Number of peptides: 15169 | gene expression, regeneration, annotation, expression data, peptide sequence, gene sequence, tissue regeneration, newt, pathway, mammal, blast, contigs, peptide, tissue, microarray, heart, lens, dorsal, ventral, transcript, functional annotation, molecular process, model organism, expressed sequence tag, sequence, mass spectrometry, protein, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Max Planck Institute for Heart and Lung Research; Bad Nauheim; Germany |
Hessian Ministry for Science and Art | PMID:22039101 | To be used only for research and educational purposes. Any reproduction or use for commercial purpose is prohibited without the prior express written permission of the MPI for heart and lung research. | nlx_151479, biotools:newt-omics | https://bio.tools/newt-omics | SCR_006073 | newt db, Newt database | 2026-09-12 12:56:35 | 1 | ||||
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NEMBASE Resource Report Resource Website 10+ mentions |
NEMBASE (RRID:SCR_006070) | NEMBASE | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | NEMBASE is a comprehensive Nematode Transcriptome Database including 63 nematode species, over 600,000 ESTs and over 250,000 proteins. Nematode parasites are of major importance in human health and agriculture, and free-living species deliver essential ecosystem services. The genomics revolution has resulted in the production of many datasets of expressed sequence tags (ESTs) from a phylogenetically wide range of nematode species, but these are not easily compared. NEMBASE4 presents a single portal into extensively functionally annotated, EST-derived transcriptomes from over 60 species of nematodes, including plant and animal parasites and free-living taxa. Using the PartiGene suite of tools, we have assembled the publicly available ESTs for each species into a high-quality set of putative transcripts. These transcripts have been translated to produce a protein sequence resource and each is annotated with functional information derived from comparison with well-studied nematode species such as Caenorhabditis elegans and other non-nematode resources. By cross-comparing the sequences within NEMBASE4, we have also generated a protein family assignment for each translation. The data are presented in an openly accessible, interactive database. An example of the utility of NEMBASE4 is that it can examine the uniqueness of the transcriptomes of major clades of parasitic nematodes, identifying lineage-restricted genes that may underpin particular parasitic phenotypes, possible viral pathogens of nematodes, and nematode-unique protein families that may be developed as drug targets. | nematode, transcriptome, expressed sequence tag, protein, cluster, library, sequence, peptide prediction, functional annotation, gene family, gene, annotation, pathway, genome, partigene, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: nematodes.org |
Wellcome Trust ; Hospital for Sick Children ; BBSRC ; MRC ; NERC |
PMID:21550347 PMID:14681449 |
Public | nlx_151476, biotools:nembase4 | https://bio.tools/nembase4 | SCR_006070 | NEMBASE4, NEMBASE4 - Nematode Transcriptome Analyses | 2026-09-12 12:56:35 | 25 | ||||
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HFV Database Resource Report Resource Website 1+ mentions |
HFV Database (RRID:SCR_006017) | HFV Database | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | The Hemorrhagic Fever Viruses (HFV) sequence database collects and stores sequence data and provides a user-friendly search interface and a large number of sequence analysis tools, following the model of the highly regarded and widely used Los Alamos HIV database. The database uses an algorithm that aligns each sequence to a species-wide reference sequence. The NCBI RefSeq database is used for this; if a reference sequence is not available, a Blast search finds the best candidate. Using this method, sequences in each genus can be retrieved pre-aligned. Hemorrhagic fever viruses (HFVs) are a diverse set of over 80 viral species, found in 10 different genera comprising five different families: arena-, bunya-, flavi-, filo- and togaviridae. All these viruses are highly variable and evolve rapidly, making them elusive targets for the immune system and for vaccine and drug design. About 55,000 HFV sequences exist in the public domain today. A central website that provides annotated sequences and analysis tools will be helpful to HFV researchers worldwide. | gene, hemorrhagic fever virus, biothreat, virus, sequence, nucleotide sequence, reference sequence, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: RefSeq has parent organization: HIV Databases |
United States Department of Defense contract HDTRA B084498I | PMID:22064861 | biotools:hfv, nlx_151408 | https://bio.tools/hfv | SCR_006017 | HFV Sequence Database, Hemorrhagic Fever Viruses Database, Hemorrhagic Fever Viruses (HFV) Database, LANL hemorrhagic fever virus database, Hemorrhagic Fever Viruses (HFV) Database Project | 2026-09-12 12:56:34 | 1 |
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The data sets included in this resource are published in Kravitz et al, 2012. Distinct roles for direct and indirect pathway striatal neurons in reinforcement (Nat. Neurosci).
