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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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GeneWindow Resource Report Resource Website 1+ mentions |
GeneWindow (RRID:SCR_008183) | data analysis software, data processing software, software application, software resource | Software tool for pre- and post-genetic bioinformatics and analytical work, developed and used at the Core Genotyping Facility (CGF) at the National Cancer Institute. While Genewindow is implemented for the human genome and integrated with the CGF laboratory data, it stands as a useful tool to assist investigators in the selection of variants for study in vitro, or in novel genetic association studies. The Genewindow application and source code is publicly available for use in other genomes, and can be integrated with the analysis, storage, and archiving of data generated in any laboratory setting. This can assist laboratories in the choice and tracking of information related to genetic annotations, including variations and genomic positions. Features of GeneWindow include: -Intuitive representation of genomic variation using advanced web-based graphics (SVG) -Search by HUGO gene symbol, dbSNP ID, internal CGF polymorphism ID, or chromosome coordinates -Gene-centric display (only when a gene of interest is in view) oriented 5 to 3 regardless of the reference strand and adjacent genes -Two views, a Locus Overview, which varies in size depending on the gene or genomic region being viewed and, below it, a Sequence View displaying 2000 base pairs within the overview -Navigate the genome by clicking along the gene in the Locus Overview to change the Sequence View, expand or contract the genomic interval, or shift the view in the 5 or 3 direction (relative to the current gene) -Lists of available genomic features -Search for sequence matches in the Locus Overview -Genomic features are represented by shape, color and opacity with contextual information visible when the user moves over or clicks on a feature -Administrators can insert newly-discovered polymorphisms into the Genewindow database by entering annotations directly through the GUI -Integration with a Laboratory Information Management System (LIMS) or other databases is possible | gene, genetic, analysis, annotation, archive, bioinformatic, cancer, genome, genomic, genotype, genotyping, human, human genome databases, maps, polymorphism, position, variation, data set |
is listed by: 3DVC has parent organization: National Cancer Institute |
nif-0000-21173 | SCR_008183 | GeneWindow | 2026-08-29 11:23:00 | 1 | |||||||||
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Informatics for Integrating Biology and the Bedside Resource Report Resource Website 10+ mentions |
Informatics for Integrating Biology and the Bedside (RRID:SCR_013629) | i2b2 | data or information resource, data set, organization portal, portal, software resource, training resource | i2b2 (Informatics for Integrating Biology and the Bedside) is an NIH-funded National Center for Biomedical Computing based at Partners HealthCare System. The i2b2 Center is developing a scalable informatics framework that will enable clinical researchers to use existing clinical data for discovery research and, when combined with IRB-approved genomic data, facilitate the design of targeted therapies for individual patients with diseases having genetic origin. For some resources (e.g. software) the use of the resource requires accepting a specific (e.g. OpenSource) license. | genetic, biology, biomedical, computing, genomic, health, healthcare, informatic, origin, patient, therapy, predoctoral, postdoctoral |
is related to: National Centers for Biomedical Computing is parent organization of: i2b2 Cross-Institutional Clinical Translational Research project is parent organization of: Smoking NLP Challenge Data |
NLM U54LM008748 | Free, Public, Acknowledgement requested | nif-0000-33133 | SCR_013629 | 2026-08-29 11:24:39 | 30 | |||||||
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European large-scale functional genomics in the rat for translational research (EURATRANS) Resource Report Resource Website 1+ mentions |
European large-scale functional genomics in the rat for translational research (EURATRANS) (RRID:SCR_013697) | EURATRANS | consortium, data or information resource, organization portal, portal | The European large-scale functional genomics in the rat for translational research (EURATRANS) consortium brings together investigators who will use next-generation sequencing technologies to generate genomic, transcriptomic and epigenomic datasets. The goal is to create quantitative metabonomic and proteomic datasets to give significant depth of coverage, at multiple levels, across pathophysiological phenotypes. The aim is to enable insights into disease mechanisms, through an integrative, cross-disciplinary approach to understanding large-scale functional genomic datasets in rats and humans. | government, individual consortium, basic science, tool development, biomarker research, data-sharing enabler, genomic, transcriptomic, epigenomic, rat, | European Union FP7 n HEALTH-F4-2010-241504 | SCR_013697 | 2026-08-29 11:24:41 | 1 | ||||||||||
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Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Bioinformatics Resource Resource Report Resource Website |
Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Bioinformatics Resource (RRID:SCR_015324) | access service resource, analysis service resource, core facility, data or information resource, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 27,2022. Core provides bioinformatics specialists available to assist researchers with processing, exploring, and understanding genomics data. | hematology, bioinformatics, explore, understand, genomic, data, cancer |
is listed by: NIDDK Information Network (dkNET) has parent organization: Fred Hutchinson Cancer Center |
Cancer | NIDDK P30 DK056465 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015907 | SCR_015324 | Hutch, Bioinformatic Resource, Fred, Co-operative Center for Excellence in Hematology, Cancer Center | 2026-08-29 11:24:57 | 0 | ||||||
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Mouse Genome Databases Resource Report Resource Website 1+ mentions |
Mouse Genome Databases (RRID:SCR_007147) | MGD | data or information resource, data set, database, organism-related portal, portal, topical portal | A mouse-related portal of genomic databases and tables of mouse brain data. Most files are intended for you to download and use on your own personal computer. Most files are available in generic text format or as FileMaker Pro databases. The server provides data extracted and compiled from: The 2000-2001 Mouse Chromosome Committee Reports, Release 15 of the MIT microsatellite map (Oct 1997), The recombinant inbred strain database of R.W. Elliott (1997) and R. W. Williams (2001), and the Map Manager and text format chromosome maps (Apr 2001). * LXS genotype (Excel file): Updated, revised positions for 330 markers genotyped using a panel of 77 LXS strain. * MIT SNP DATABASE ONLINE: Search and sort the MIT Single Nucleotide Polymorphism (SNP) database ONLINE. These data from the MIT-Whitehead SNP release of December 1999. * INTEGRATED MIT-ROCHE SNP DATABASE in EXCEL and TEXT FORMATS (1-3 MB): Original MIT SNPs merged with the new Roche SNPs. The Excel file has been formatted to illustrate SNP haplotypes and genetic contrasts. Both files are intended for statistical analyses of SNPs and can be used to test a method outlined in a paper by Andrew Grupe, Gary Peltz, and colleagues (Science 291: 1915-1918, 2001). The Excel file includes many useful equations and formatting that will help in navigating through this large database and in testing the in silico mapping method. * Use of inbred strains for the study of individual differences in pain related phenotypes in the mouse: Elissa J. Chesler''s 2002 dissertation, discussing issues relevant to the integration of genomic and phenomic data from standard inbred strains including genetic interactions with laboratory environmental conditions and the use of various in silico inbred strain haplotype based mapping algorithms for QTL analysis. * SNP QTL MAPPER in EXCEL format (572 KB, updated January 2002 by Elissa Chesler): This Excel workbook implements the Grupe et al. mapping method and outputs correlation plots. The main spreadsheet allows you to enter your own strain data and compares them to haplotypes. Be very cautious and skeptical when using this spreadsheet and the technique. Read all of the caveates. This excel version of the method was developed by Elissa Chesler. This updated version (Jan 2002) handles missing data. * MIT SNP Database (tab-delimited text format): This file is suitable for manipulation in statistics and spreadsheet programs (752 KB, Updated June 27, 2001). Data have been formatted in a way that allows rapid acquisition of the new data from the Roche Bioscience SNP database. * MIT SNP Database (FileMaker 5 Version): This is a reformatted version of the MIT Single Nucleotide Polymorphism (SNP) database in FileMaker 5 format. You will need a copy of this application to open the file (Mac and Windows; 992 KB. Updated July 13, 2001 by RW). * Gene Mapping and Map Manager Data Sets: Genetic maps of mouse chromosomes. Now includes a 10th generation advanced intercross consisting of 500 animals genetoyped at 340 markers. Lots of older files on recombinant inbred strains. * The Portable Dictionary of the Mouse Genome, 21,039 loci, 17,912,832 bytes. Includes all 1997-98 Chromosome Committee Reports and MIT Release 15. * FullDict.FMP.sit: The Portable Dictionary of the Mouse Genome. This large FileMaker Pro 3.0/4.0 database has been compressed with StuffIt. The Dictionary of the Mouse Genome contains data from the 1997-98 chromosome committee reports and MIT Whitehead SSLP databases (Release 15). The Dictionary contains information for 21,039 loci. File size = 4846 KB. Updated March 19, 1998. * MIT Microsatellite Database ONLINE: A database of MIT microsatellite loci in the mouse. Use this FileMaker Pro database with OurPrimersDB. MITDB is a subset of the Portable Dictionary of the Mouse Genome. ONLINE. Updated July 12, 2001. * MIT Microsatellite Database: A database of MIT microsatellite loci in the mouse. Use this FileMaker Pro database with OurPrimersDB. MITDB is a subset of the Portable Dictionary of the Mouse Genome. File size = 3.0 MB. Updated March 19, 1998. * OurPrimersDB: A small database of primers. Download this database if you are using numerous MIT primers to map genes in mice. This database should be used in combination with the MITDB as one part of a relational database. File size = 149 KB. Updated March 19, 1998. * Empty copy (clone) of the Portable Dictionary in FileMaker Pro 3.0 format. Download this file and import individual chromosome text files from the table into the database. File size = 231 KB. Updated March 19, 1998. * Chromosome Text Files from the Dictionary: The table lists data on gene loci for individual chromosomes. | gene, genetic, chromosome, genotype, inbred mouse strain, pain, phenotype, polygenic, recombinant, trait, genome, genomic, single nucleotide polymorphism, primer, brain, recombinant inbred mouse strain |
has parent organization: University of Tennessee Health Science Center; Tennessee; USA is organization facet of: Alliance of Genome Resources |
nif-0000-20982 | SCR_007147 | 2026-08-29 11:23:02 | 2 | |||||||||
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Tetraodon Genome Browser Resource Report Resource Website 1+ mentions |
Tetraodon Genome Browser (RRID:SCR_007079) | data or information resource, database, portal, topical portal | The initial objective of Genoscope was to compare the genomic sequences of this fish to that of humans to help in the annotation of human genes and to estimate their number. This strategy is based on the common genetic heritage of the vertebrates: from one species of vertebrate to another, even for those as far apart as a fish and a mammal, the same genes are present for the most part. In the case of the compact genome of Tetraodon, this common complement of genes is contained in a genome eight times smaller than that of humans. Although the length of the exons is similar in these two species, the size of the introns and the intergenic sequences is greatly reduced in this fish. Furthermore, these regions, in contrast to the exons, have diverged completely since the separation of the lineages leading to humans and Tetraodon. The Exofish method, developed at Genoscope, exploits this contrast such that the conserved regions which can be identified by comparing genomic sequences of the two species, correspond only to coding regions. Using preliminary sequencing results of the genome of Tetraodon in the year 2000, Genoscope evaluated the number of human genes at about 30,000, whereas much higher estimations were current. The progress of the annotation of the human genome has since supported the Genoscope hypothesis, with values as low as 22,000 genes and a consensus of around 25,000 genes. The sequencing of the Tetraodon genome at a depth of about 8X, carried out as a collaboration between Genoscope and the Whitehead Institute Center for Genome Research (now the Broad Institute), was finished in 2002, with the production of an assembly covering 90 of the euchromatic region of the genome of the fish. This has permitted the application of Exofish at a larger scale in comparisons with the genome of humans, but also with those of the two other vertebrates sequenced at the time (Takifugu, a fish closely related to Tetraodon, and the mouse). The conserved regions detected in this way have been integrated into the annotation procedure, along with other resources (cDNA sequences from Tetraodon and ab initio predictions). Of the 28,000 genes annotated, some families were examined in detail: selenoproteins, and Type 1 cytokines and their receptors. The comparison of the proteome of Tetraodon with those of mammals has revealed some interesting differences, such as a major diversification of some hormone systems and of the collagen molecules in the fish. A search for transposable elements in the genomic sequences of Tetraodon has also revealed a high diversity (75 types), which contrasts with their scarcity; the small size of the Tetraodon genome is due to the low abundance of these elements, of which some appear to still be active. Another factor in the compactness of the Tetraodon genome, which has been confirmed by annotation, is the reduction in intron size, which approaches a lower limit of 50-60 bp, and which preferentially affects certain genes. The availability of the sequences from the genomes of humans and mice on one hand, and Takifugu and Tetraodon on the other, provide new opportunities for the study of vertebrate evolution. We have shown that the level of neutral evolution is higher in fish than in mammals. The protein sequences of fish also diverge more quickly than those of mammals. A key mechanism in evolution is gene duplication, which we have studied by taking advantage of the anchoring of the majority of the sequences from the assembly on the chromosomes. The result of this study speaks strongly in favor of a whole genome duplication event, very early in the line of ray-finned fish (Actinopterygians). An even stronger evidence came from synteny studies between the genomes of humans and Tetraodon. Using a high-resolution synteny map, we have reconstituted the genome of the vertebrate which predates this duplication - that is, the last common ancestor to all bony vertebrates (most of the vertebrates apart from cartilaginous fish and agnaths like lamprey). This ancestral karyotype contains 12 chromosomes, and the 21 Tetraodon chromosomes derive from it by the whole genome duplication and a surprisingly small number of interchromosomal rearrangements. On the contrary, exchanges between chromosomes have been much more frequent in the lineage that leads to humans. Sponsors: The project was supported by the Consortium National de Recherche en Genomique and the National Human Genome Research Institute. | duplication, element, euchromatic, evolution, exon, fish, gene, genetic, actinopterygians, aganth, ancestor, cartilaginous, cdna, chromosome, coding, collagen, cytokine, diversity, genome, genomic, heritage, hormone, human, interchromossomal, intergenic, intron, karyotype, lineage, mammal, molecule, mouse, nigroviridis, protein, proteome, pufferfish, receptor, region, selenoprotein, sequence, size, specie, synteny, system, takifugu, tetraodon, transposable, vertebrate | nif-0000-20997 | SCR_007079 | TGB | 2026-08-29 11:22:46 | 8 | ||||||||||
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Broad Institute Resource Report Resource Website 1000+ mentions |
Broad Institute (RRID:SCR_007073) | Broad | institution | Biomedical and genomic research center located in Cambridge, Massachusetts, United States. Nonprofit research organization under the name Broad Institute Inc., and is partners with Massachusetts Institute of Technology, Harvard University, and the five Harvard teaching hospitals. Dedicated to advance understanding of biology and treatment of human disease to improve human health. | biomedical, genomic, research, center, nonprofit, organization, human, biology, disease |
is affiliated with: Massachusetts Institute of Technology; Massachusetts; USA; is affiliated with: Harvard University; Cambridge; United States is affiliated with: Integrative Human Microbiome Project is affiliated with: MIT; Cambridge; Massachusetts; United States is related to: LINCS Information Framework is related to: HMS LINCS Database is related to: Cancer Cell Line Encyclopedia is related to: GO2MSIG is parent organization of: ARACHNE is parent organization of: MuTect is parent organization of: SiPhy is parent organization of: ContEst is parent organization of: Broad Minded is parent organization of: JBrowse is parent organization of: Birdseed is parent organization of: VAAL is parent organization of: SomaticCall is parent organization of: BIRDSUITE is parent organization of: GATK is parent organization of: SNAP - SNP Annotation and Proxy Search is parent organization of: SYZYGY is parent organization of: Genetic Maps of the Rat Genome is parent organization of: LINCS Connectivity Map is parent organization of: Classification of Human Lung Carcinomas by mRNA Expression Profiling Reveals Distinct Adenocarcinoma Sub-classes is parent organization of: Haploview is parent organization of: Magnaporthe comparative Database is parent organization of: GeneCruiser is parent organization of: Fungal Genome Initiative is parent organization of: Gene Set Enrichment Analysis is parent organization of: GenePattern is parent organization of: MAGENTA is parent organization of: Multiple Myeloma Genomics Portal is parent organization of: ExAc is parent organization of: Ricopili is parent organization of: UnifiedGenotyper is parent organization of: SomaticIndelDetector is parent organization of: RNA-SeQC is parent organization of: Oncotator is parent organization of: ABSOLUTE is parent organization of: PathSeq is parent organization of: V-Phaser 2 is parent organization of: Indelocator is parent organization of: Scripture is parent organization of: VICUNA is parent organization of: Tuberculosis Database is parent organization of: HaploReg is parent organization of: CellProfiler Image Analysis Software is parent organization of: National Institute of Mental Health (NIMH) Human Genetics Initiative is parent organization of: ChemBank is parent organization of: GeneCluster 2: An Advanced Toolset for Bioarray Analysis is parent organization of: Ultrasome is parent organization of: Diabetes Genetics Initiative is parent organization of: Dog Genome Project is parent organization of: Gene Relationships Across Implicated Loci is parent organization of: InVEx is parent organization of: Broad Genetic Analysis Platform is parent organization of: CellProfiler Analyst is parent organization of: ALLPATHS-LG is parent organization of: MutSig is parent organization of: SegSeq is parent organization of: Argo Genome Browser is parent organization of: Integrative Genomics Viewer is parent organization of: MEDEA is parent organization of: Pathline is parent organization of: ASPGD is parent organization of: DGAP is parent organization of: BARD is parent organization of: 1000 Genomes: A Deep Catalog of Human Genetic Variation is parent organization of: Trinity is parent organization of: Genome Aggregation Database is parent organization of: GenomeSpace is parent organization of: Picard is parent organization of: Connectivity Map 02 is parent organization of: CMap is parent organization of: IndelGenotyper is parent organization of: Discovar assembler is parent organization of: Molecular Signatures Database is parent organization of: GSEA is parent organization of: Eagle is parent organization of: Morpheus by Broad Institute is parent organization of: Cancer Dependency Map Portal is parent organization of: LIGER is parent organization of: Drop-seq tools is parent organization of: scATAC Pipeline is parent organization of: Guide Design Resources is parent organization of: Smart-seq2 Single Sample Pipeline is parent organization of: Smart-seq2 Single Nucleus Multi Sample Pipeline is parent organization of: Broad Terra cloud commons for pathogen surveillance is parent organization of: Single Cell Portal is parent organization of: CEMBA MethylC Seq Pipeline is parent organization of: Pegasus is parent organization of: Cumulus is parent organization of: Cirrocumulus is parent organization of: BICCN Anatomy and Morphology Project is parent organization of: Terra is parent organization of: JUMP Cell Painting Consortium is parent organization of: Spectrum Mill is parent organization of: Polysolver is parent organization of: Brain Cell Data Viewer is parent organization of: Eagle is parent organization of: Broad Institute Imaging Platform Core Facility is parent organization of: ATAC Pipeline is parent organization of: ichorCNA is parent organization of: CRISPick is parent organization of: FireBrowse is parent organization of: Cellarium is parent organization of: multiVIB is parent organization of: SlideTags.wdl is parent organization of: Slide-seq Pipeline is parent organization of: BuildIndices is parent organization of: Broad Institute Genomics Platform has organization facet: GATK HaplotypeCaller has organization facet: GATK VariantFiltration |
Eli and Edythe Broad ; individual donors |
nif-0000-31438, grid.66859.34, Wikidata: Q4971893 | https://ror.org/05a0ya142 | SCR_007073 | Broad Institute of MIT and Harvard, Broad Institute Inc. | 2026-08-29 11:22:46 | 1931 | ||||||
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DISULFIND Resource Report Resource Website 50+ mentions |
DISULFIND (RRID:SCR_016072) | Disulfinder | data analysis software, data processing software, sequence analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023, Software for predicting the disulfide bonding state of cysteines and their disulfide connectivity, starting from a protein sequence alone and may be useful in other genomic annotation tasks. | predict, disulfide, bonding, state, cysteine, protein, sequence, genomic, annotation, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools has parent organization: University of Florence; Florence; Italy |
Embark Fellowship from the Irish Research Council for Science ; Engineering and Technology ; EU NoE BIOPATTERN contract no. FP6-508803; EU STREP APrIL II contract no. FP6-508861 |
PMID:16844986 DOI:10.1093/nar/gkl266 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04214, biotools:disulfind | https://bio.tools/disulfind, https://sources.debian.org/src/disulfinder/ | SCR_016072 | Cysteines Disulfide Bonding State and Connectivity Predictor | 2026-08-29 11:25:30 | 71 | ||||
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Cassiopee Resource Report Resource Website |
Cassiopee (RRID:SCR_016056) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software to scan an input genomic sequence (dna/rna/protein). It searchs for a subsequence that has an exact match, substitutions (Hamming distance), and/or insertion/deletions with supporting alphabet ambiguity. | genomic, sequence, DNA, RNA, protein, scan, subsequence, search, match, substitution, distance, Hamming, insertion, deletion |
is listed by: Debian is listed by: OMICtools has parent organization: Durham University; Durham; England |
Free, Available for download | OMICS_19794 | https://sources.debian.org/src/cassiopee/ | SCR_016056 | cassiopee-c | 2026-08-29 11:25:06 | 0 | |||||||
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NeMOarchive Resource Report Resource Website 100+ mentions |
NeMOarchive (RRID:SCR_016152) | NeMO | data or information resource, data repository, database, service resource, storage service resource | Data repository specifically focused on storage and dissemination of omic data generated from BRAIN Initiative and related brain research projects. Data repository and archive for BCDC and BICCN project, among others. NeMO data include genomic regions associated with brain abnormalities and disease, transcription factor binding sites and other regulatory elements, transcription activity, levels of cytosine modification, histone modification profiles and chromatin accessibility. | omic, neuroscience, neurobiology, bcbc, biccn, nih, brain, genomic, region, abnormal, transcription, factor, binding, site, chromatin, regulatory, element, data |
is used by: BRAIN Initiative Cell Atlas Network is used by: BICCN is recommended by: BRAIN Initiative is related to: NeMO Analytics has parent organization: University of Maryland School of Medicine; Maryland; USA |
BRAIN Initiative ; NIMH MH114788 |
Free, Freely available | https://data.nemoarchive.org/ | SCR_016152 | NeMO Archive, Neuroscience Multi-omic Data Archive, The Neuroscience Multi-Omic Archive, Neuroscience Multi-Omic Archive | 2026-08-29 11:25:32 | 126 | ||||||
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Gff2aplot Resource Report Resource Website |
Gff2aplot (RRID:SCR_016128) | data processing software, data visualization software, software application, software resource | Software application to visualize the alignment of two genomic sequences together with their annotations. Used to generate print-quality images for comparative genome sequence analysis. | alignment, pair-wise, plot, genomic, sequence, visualize, together, annotate, analysis, parameter, dataset, |
is listed by: Debian is listed by: OMICtools |
PMID:14668236 | Free, Available for download | OMICS_19949 | https://sources.debian.org/src/gff2aplot/ | SCR_016128 | 2026-08-29 11:25:13 | 0 | |||||||
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GOTrack Resource Report Resource Website 1+ mentions |
GOTrack (RRID:SCR_016399) | data access protocol, data or information resource, database, software resource, web service | Open source web-based system and database that provides access to historical records and trends in the Gene Ontology (GO) and GO annotations (GOA). Used for monitoring changes in the Gene Ontology and their impact on genomic data analysis. | database, system, access, historical, monitor, record, gene, genomic, data, analysis, ontology, annotation, bioinformatics |
is listed by: OMICtools is related to: University of British Columbia; British Columbia; Canada |
Canadian Foundation for Innovation infrastructure ; CIHR ; NIH MH111099; NSERC Discovery Grant |
DOI:10.1101/320861 | Free, Available for download, Freely available | https://github.com/PavlidisLab/gotrack, https://omictools.com/gotrack-tool | SCR_016399 | 2026-08-29 11:25:13 | 1 | |||||||
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PRISM (Stanford database) Resource Report Resource Website 10000+ mentions |
PRISM (Stanford database) (RRID:SCR_005375) | PRISM | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5,2022.Tool that predicts interactions between transcription factors and their regulated genes from binding motifs. Understanding vertebrate development requires unraveling the cis-regulatory architecture of gene regulation. PRISM provides accurate genome-wide computational predictions of transcription factor binding sites for the human and mouse genomes, and integrates the predictions with GREAT to provide functional biological context. Together, accurate computational binding site prediction and GREAT produce for each transcription factor: 1. putative binding sites, 2. putative target genes, 3. putative biological roles of the transcription factor, and 4. putative cis-regulatory elements through which the factor regulates each target in each functional role., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | genomic, transcription factor, function, transcription factor binding site, transcription factor regulator, biological role, target gene, target genomic region, genome, FASEB list |
is listed by: OMICtools is listed by: SoftCite is related to: GREAT: Genomic Regions Enrichment of Annotations Tool has parent organization: Stanford University School of Medicine; California; USA |
PMID:23382538 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00489 | SCR_005375 | Predicting Regulatory Information from Single Motifs | 2026-08-29 11:22:19 | 40822 | ||||||
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MolBioLib Resource Report Resource Website |
MolBioLib (RRID:SCR_005372) | MolBioLib | software resource | A compact, portable, and extensively tested C++11 software framework and set of applications tailored to the demands of next-generation sequencing data and applicable to many other applications. It is designed to work with common file formats and data types used both in genomic analysis and general data analysis. A central relational-database-like Table class is a flexible and powerful object to intuitively represent and work with a wide variety of tabular datasets, ranging from alignment data to annotations. MolBioLib includes programs to perform a wide variety of analysis tasks such as computing read coverage, annotating genomic intervals, and novel peak calling with a wavelet algorithm. This package assumes fluency in both UNIX and C++. | c++, next-generation sequencing, genomic, analysis, genome |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22815363 | OMICS_01145 | SCR_005372 | MolBioLib: C++11 framework for rapid develop and deploy of bioinformatic tasks | 2026-08-29 11:22:19 | 0 | |||||||
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KGGSeq Resource Report Resource Website 50+ mentions |
KGGSeq (RRID:SCR_005311) | KGGSeq | software resource | A biological Knowledge-based mining platform for Genomic and Genetic studies using Sequence data. The software platform, constituted of bioinformatics and statistical genetics functions, makes use of valuable biologic resources and knowledge for sequencing-based genetic mapping of variants / genes responsible for human diseases / traits. It facilitates geneticists to fish for the genetic determinants of human diseases / traits in the big sea of DNA sequences. KGGSeq has paid attention to downstream analysis of genetic mapping. The framework was implemented to filter and prioritize genetic variants from whole exome sequencing data. | genomic, genetic, sequence, mutation, exome sequencing, disease, gene, variant, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Monogenic disorder, Cancer | PMID:22241780 | biotools:kggseq, OMICS_02260 | https://bio.tools/kggseq | SCR_005311 | KGGSeq: A biological Knowledge-based mining platform for Genomic and Genetic studies using Sequence data | 2026-08-29 11:22:18 | 58 | |||||
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Hydra Resource Report Resource Website 100+ mentions |
Hydra (RRID:SCR_005260) | Hydra | software resource | Software that detects structural variation (SV) breakpoints by clustering discordant paired-end alignments whose signatures corroborate the same putative breakpoint. Hydra can detect breakpoints caused by all classes of structural variation. Moreover, it was designed to detect variation in both unique and duplicated genomic regions; therefore, it will examine paired-end reads having multiple discordant alignments. Hydra does not attempt to classify SV breakpoints based on the mapping distances and orientations of each breakpoint cluster, it merely detects and reports breakpoints. This is an intentional decision, as it was observed that in loci affected by complex rearrangements, the type of variant suggested by the breakpoint signature is not always correct. Hydra does report the orientations, distances, number of supporting read-pairs, etc., for each breakpoint. It is suggested that downstream methods be used to classify variants based on the genomic features that they overlap and the co-occurrence of other breakpoints. For example, they developed BEDTools for exactly this purpose and the breakpoints reported by Hydra are in the BEDPE format used by BEDTools. Future releases of Hydra will include scripts that assist in the classification process. | structural variation, genome, genomic, breakpoint, c++, cnv, pem, paired-end, segmental duplication, rearrangement |
is listed by: OMICtools is listed by: SoftCite is related to: BEDTools has parent organization: Google Code has parent organization: University of Virginia; Virginia; USA |
OMICS_00318 | SCR_005260 | hydra-sv | 2026-08-29 11:22:11 | 119 | ||||||||
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CpG MPs Resource Report Resource Website |
CpG MPs (RRID:SCR_005441) | CpG_MPs | analysis service resource, data analysis service, production service resource, service resource, software resource | Tool for identification and analysis of CpG methylation patterns of genomic regions from high-throughput bisulfite sequencing data. It may identify the unmethylated and methylated regions for a single sample, the conserved and differential methylation regions with different methylation patterns for paired or multiple samples. It includes four main modules as follows: # Normalization of the sequencing reads of cytosines following guanines; # Identification of the unmethylated (methylated) regions using hotspot extension algorithm; # Identification of conservatively and differentially methylated regionsby combining the combinatorial algorithm for determination of potentially functional regions with the algorithm of analysis of variance (ANOVA) for assess the statistical significance of differentially methylated regions; # Extraction of sequence features and visualization of these potentially functional regions. | genomic methylation pattern, genomic, methylation pattern, java |
is listed by: OMICtools has parent organization: Harbin Medical University; Heilongjiang; China |
OMICS_00596 | SCR_005441 | CpG_MPs: identification of CpG methylation patterns of genomic regions | 2026-08-29 11:22:20 | 0 | ||||||||
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GARBAN Resource Report Resource Website |
GARBAN (RRID:SCR_005778) | GARBAN | analysis service resource, data analysis service, production service resource, service resource, software resource, source code | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 12, 2012. GARBAN is a tool for analysis and rapid functional annotation of data arising from cDNA microarrays and proteomics techniques. GARBAN has been implemented with bioinformatic tools to rapidly compare, classify, and graphically represent multiple sets of data (genes/ESTs, or proteins), with the specific aim of facilitating the identification of molecular markers in pathological and pharmacological studies. GARBAN has links to the major genomic and proteomic databases (Ensembl, GeneBank, UniProt Knowledgebase, InterPro, etc.), and follows the criteria of the Gene Ontology Consortium (GO) for ontological classifications. Source may be shared: e-mail garban (at) ceit.es. Platform: Online tool | cdna microarray, proteomics, cdna, microarray, statistical analysis, gene, est, protein, genomic, gene ontology |
is listed by: Gene Ontology Tools is related to: Gene Ontology |
PMID:14594726 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149247 | http://garban.tecnun.es | SCR_005778 | Genomic Analysis and Rapid Biological ANnotation, University of Navarra; Pamplona; Spain | 2026-08-29 11:22:24 | 0 | |||||
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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 | 2026-08-29 11:22:26 | 2 | |||||
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GREAT: Genomic Regions Enrichment of Annotations Tool Resource Report Resource Website 50+ mentions |
GREAT: Genomic Regions Enrichment of Annotations Tool (RRID:SCR_005807) | GREAT | analysis service resource, data analysis service, production service resource, service resource, software resource, source code | Data analysis service that predicts functions of cis-regulatory regions identified by localized measurements of DNA binding events across an entire genome. Whereas previous methods took into account only binding proximal to genes, GREAT is able to properly incorporate distal binding sites and control for false positives using a binomial test over the input genomic regions. GREAT incorporates annotations from 20 ontologies and is available as a web application. The utility of GREAT extends to data generated for transcription-associated factors, open chromatin, localized epigenomic markers and similar functional data sets, and comparative genomics sets. Platform: Online tool | term enrichment, cis-regulatory region, function, gene, genomic, annotation, ontology, chromatin immunoprecipitation, sequencing, chip-seq, comparative genomics, transcription factor binding |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: PRISM (Stanford database) is related to: Gene Ontology has parent organization: Stanford University School of Medicine; California; USA |
Bio-X ; Howard Hughes Medical Institute ; Stanford University; California; USA ; Packard ; Searle Scholar ; Microsoft Research ; Alfred P. Sloan Foundation ; Edward Mallinckrodt Jr. Foundation ; NIH ; Human Frontier Science Program fellowship LT000896/2009-l; NICHD 1R01HD059862; NHGRI R01HG005058; NSF CCF-0939370; DFG Hi 1423/2-1 |
PMID:20436461 PMID:23814184 |
Free for academic use, Acknowledgement requested | nlx_149295, OMICS_00635 | SCR_005807 | Genomic Regions Enrichment of Annotations Tool (GREAT), Genomic Regions Enrichment of Annotations Tool | 2026-08-29 11:22:24 | 89 |
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