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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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University of Tennessee Genome Science and Technology Graduate Program Resource Report Resource Website |
University of Tennessee Genome Science and Technology Graduate Program (RRID:SCR_000038) | UTK GST, UT Knoxville GST | data or information resource, graduate program resource, organization portal, portal | Graduate School of Genome Science and Technology (GST) is a Life Science graduate program founded on two premises. First, whole-genome sequences and related large-scale datasets have transformed how we perform biological research, a trend that is gathering momentum and is anticipated to frame the way the biology research is accomplished for many years to come. Second, advances in technology, whether at the level of instrumentation, computation, or wet lab reagents, have long been a powerful driving force in biology. The GST program is home to faculty mentors from many walks of life. The virulence factors of pathogenic fungi and the engineering of photosynthetic reaction complexes for bioenergy harvesting are just two examples from the cornucopia of research projects being pursued in GST. | genome, molecular genetics, biochemistry, bioinformatics | has parent organization: University of Tennessee Knoxville; Tennessee; USA | nlx_149162 | SCR_000038 | UTK Genome Science & Technology, UT Genome Science & Technology, UT-ORNL Graduate School of Genome Science and Technology, Graduate School of Genome Science and Technology, University of Tennessee Genome Science & Technology, University of Tennessee Genome Science Technology | 2026-09-12 12:55:02 | 0 | ||||||||
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RSEM Resource Report Resource Website 100+ mentions |
RSEM (RRID:SCR_000262) | data analysis software, data processing software, software application, software resource | Software package for quantifying gene and isoform abundances from single end or paired end RNA Seq data. Accurate transcript quantification from RNA Seq data with or without reference genome. Used for accurate quantification of gene and isoform expression from RNA-Seq data. | quantifying, gene, isoform, abundance, single, end, paired, RNA seq, data, transcript, reference, genome, bio.tools |
is listed by: OMICtools is listed by: GitHub is listed by: bio.tools is listed by: Debian has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
PMID:21816040 | Free, Available for download, Freely available | OMICS_01966, OMICS_01287, biotools:rsem, SCR_013027 | https://github.com/deweylab/RSEM, https://github.com/deweylab/RSEM/releases, https://bio.tools/rsem, https://sources.debian.org/src/rsem/ | SCR_000262 | RSEM, RNA-Seq by Expectation-Maximization, RSEM-v1.3.0 | 2026-09-12 12:55:06 | 115 | ||||||
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EdgeBio Resource Report Resource Website |
EdgeBio (RRID:SCR_000183) | EdgeBio | commercial organization | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A contract research organization that provides genomics services such as sequencing, bioinformatics, NGS data analysis and whole exome sequencing. EdgeBio is a CLIA-approved service provider. | contract research organization, CRO, genomics, genome, sequencing, bioinformatics, NGS data analysis, whole exome sequencing, research, Illumina NGS | is listed by: ScienceExchange | THIS RESOURCE IS NO LONGER IN SERVICE | SciEx_203 | https://www.edgebio.com/ | SCR_000183 | Edge Bio, EdgeBio.com | 2026-09-12 12:55:04 | 0 | ||||||
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ARACHNE Resource Report Resource Website 1+ mentions |
ARACHNE (RRID:SCR_000351) | ARACHNE | software resource | A software for genome assembly, and is specifically designed to analyze long Sanger-chemistry reads. | genome, sequencing, analysis, sanger, chemistry, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Broad Institute |
PMID:11779843 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01812, biotools:arachne | https://bio.tools/arachne | SCR_000351 | ARACHNE: a whole-genome shotgun assembler, ARACHNE (Unsupported) | 2026-09-12 12:55:07 | 3 | |||||
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HudsonAlpha Genomics Services Lab Resource Report Resource Website |
HudsonAlpha Genomics Services Lab (RRID:SCR_000353) | HudsonAlpha Genomics Services Lab | service resource | A lab that offers genetic research tools such as RNA sequencing and a variety of arrays. | genome, sequencing, assembly, rna, microarray, exome | is listed by: ScienceExchange | THIS RESOURCE IS NO LONGER IN SERVICE | SciEx_221 | SCR_000353 | HudsonAlpha Institute for Biotechnology Genomics Services Lab, Genomics Services Lab | 2026-09-12 12:55:07 | 0 | |||||||
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MPscan Resource Report Resource Website |
MPscan (RRID:SCR_000587) | MPscan | data access protocol, software resource, web service | Web tool for index free mapping of multiple short reads on a genome. | linux, macos, next-generation sequencing, genome, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: ATGC: Montpellier bioinformatics platform |
Free, Available for download, Freely available | biotools:mpscan, OMICS_00670 | https://bio.tools/mpscan | SCR_000587 | MPscan: index free mapping of multiple short reads on a genome | 2026-09-12 12:55:11 | 0 | ||||||
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Pindel Resource Report Resource Website 10+ mentions |
Pindel (RRID:SCR_000560) | Pindel | software resource | Software to detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | deletion, insertion, nucleotide, genome, read, inversion, tandem duplication, structural variant, next-generation sequencing, pattern growth, indel, breakpoint, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA works with: cgpPindel |
PMID:19561018 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:pindel, OMICS_00321 | https://bio.tools/pindel | SCR_000560 | 2026-09-12 12:55:11 | 25 | ||||||
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FPSAC Resource Report Resource Website 1+ mentions |
FPSAC (RRID:SCR_000555) | FPSAC | software resource | Sogftware for fast Phylogenetic Scaffolding of Ancient Contigs. | genome, scaffolding, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Simon Fraser University; British Columbia; Canada |
PMID:24068034 | biotools:fpsac, OMICS_00041 | https://bio.tools/fpsac | SCR_000555 | Fast Phylogenetic Scaffolding of Ancient Contigs (FPSAC) and application to the medieval Black Death agent, Fast Phylogenetic Scaffolding of Ancient Contigs, FPSAC: fast phylogenetic scaffolding of ancient contigs | 2026-09-12 12:55:11 | 1 | ||||||
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POPBAM Resource Report Resource Website |
POPBAM (RRID:SCR_000464) | POPBAM | data analysis software, data processing software, software application, software resource | A tool to perform evolutionary or population-based analyses of next-generation sequencing data. POPBAM takes a BAM file as its input and can compute many widely used evolutionary genetics measures in sliding windows across a genome. | next-generation sequencing, evolution, population, bam, genome, evolutionary genetics, c++, short read, sequence alignment, sliding window, command-line, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: University of Rochester; New York; USA |
PMID:24027417 | Free, Available for download, Freely available | biotools:popbam, OMICS_01559 | https://bio.tools/popbam | http://popbam.sourceforge.net/ | SCR_000464 | 2026-09-12 12:55:10 | 0 | |||||
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Genome BioInformatics Research Lab - gff2ps Resource Report Resource Website 1+ mentions |
Genome BioInformatics Research Lab - gff2ps (RRID:SCR_000462) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software program for visualizing annotations of genomic sequences. The program has features such as the ability to create comprehensive plots, customizable parameters, and flexibility in file format. | genome, sequence, visualization, parameters, bioinformatics, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
PMID:11099262 DOI:10.1093/bioinformatics/16.8.743 |
Free, Available for download, Freely available | OMICS_17140, biotools:gff2ps, nif-0000-30611 | https://bio.tools/gff2ps, https://sources.debian.org/src/gff2ps/ | SCR_000462 | gff2ps | 2026-09-12 12:55:10 | 1 | ||||||
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Genboree Discovery System Resource Report Resource Website 10+ mentions |
Genboree Discovery System (RRID:SCR_000747) | Genboree | data or information resource, data processing software, database, software application, software resource | A software application and database viewing system for genomic research, more specifically formulti-genome comparison and pattern discovery via genome self-comparison. Data are available for a range of species including Human Chr3, Human Chr12, Sea Urchin, Tribolium, and cow. The Genboree Discovery System is the largest software system developed at the bioinformatics laboratory at Baylor in close collaboration with the Human Genome Sequencing Center. Genboree is a turnkey software system for genomic research. Genboree is hosted on the Internet and, as of early 2007, the number of registered users exceeds 600. While it can be configured to support almost any genome-centric discovery process, a number of configurations already exist for specific applications. Current focus is on enabling studies of genome variation, including array CGH studies, PCR-based resequencing, genome resequencing using comparative sequence assembly, genome remapping using paired-end tags and sequences, genome analysis and annotation, multi-genome comparison and pattern discovery via genome self-comparison. Genboree database and visualization settings, tools, and user roles are configurable to fit the needs of specific discovery processes. Private permanent project-specific databases can be accessed in a controlled way by collaborators via the Internet. Project-specific data is integrated with relevant data from public sources such as genome browsers and genomic databases. Data processing tools are integrated using a plug-in model. Genboree is extensible via flexible data-exchange formats to accommodate project specific tools and processing steps. Our Positional Hashing method, implemented in the Pash program, enables extremely fast and accurate sequence comparison and pattern discovery by employing low-level parallelism. Pash enables fast and sensitive detection of orthologous regions across mammalian genomes, and fast anchoring of hundreds of millions of short sequences produced by next-generation sequencing technologies. We are further developing the Pash program and employing it in the context of various discovery pipelines. Our laboratory participates in the pilot stage of the TCGA (The Cancer Genome Atlas) project. We aim to develop comprehensive, rapid, and economical methods for detecting recurrent chromosomal aberrations in cancer using next-generation sequencing technologies. The methods will allow detection of recurrent chromosomal aberrations in hundreds of small ( | genome, genomic, next generation sequencing |
is related to: Spark has parent organization: Baylor University; Texas; USA |
nif-0000-08906 | SCR_000747 | Genboree Discovery System | 2026-09-12 12:55:14 | 11 | ||||||||
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USP Molecular Genetics and Bioinformatics Laboratory Resource Report Resource Website 1+ mentions |
USP Molecular Genetics and Bioinformatics Laboratory (RRID:SCR_000605) | USP Molecular Genetics and Bioinformatics Laboratory | data or information resource, laboratory portal, organization portal, portal | Laboratory portal of the University of Sao Paulo Molecular Genetics and Bioinformatic Laboratory. | genetics, bioinformatics, data mining, genome, gene | has parent organization: University of Sao Paulo; Sao Paulo; Brazil | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149158 | SCR_000605 | University of Sao Paulo Molecular Genetics and Bioinformatic Laboratory, USP Laboratorio de Genetica Molecular e Bioinformatica, University of Sao Paulo Molecular Genetics and Bioinformatics Laboratory, USP Molecular Genetics Bioinformatics Laboratory, USP Molecular Genetics and Bioinformatic Laboratory | 2026-09-12 12:55:12 | 1 | |||||||
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GRS Resource Report Resource Website 1+ mentions |
GRS (RRID:SCR_001008) | data analysis software, data management software, data processing software, software application, software resource | A compression tool for efficient storage of Genome Re-Sequencing data. GRS processes genome sequence data without use of reference SNPs and other variants. It can also automatically rebuild the individual genome sequence data using the reference genome sequence. | data analysis software, data management software, compression tool, data compression, storage, genome, resequencing | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00960 | SCR_001008 | 2026-09-12 01:00:07 | 2 | |||||||||
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NTAP Resource Report Resource Website 10+ mentions |
NTAP (RRID:SCR_001488) | NTAP | data analysis software, data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software for tiling array data analysis to survey the genome-wide binding sites of transcription factor HY5 in Arabidopsis and the genome-wide histone modifications/DNA methylation level in rice. It was developed in the process of generating NimbleGen analysis. Written in R and Perl. | software, tiling array, data analysis, rice, arabidopsis, hy5, transcription factor, genome |
is listed by: OMICtools has parent organization: Peking University; Beijing; China |
PMID:19468055 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00808 | SCR_001488 | NimbleGen Tiling array Analysis Package, NimbleGen Tilingarray Analysis Package | 2026-09-12 01:00:07 | 10 | ||||||
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Pathosystems Resource Integration Center Resource Report Resource Website 1000+ mentions |
Pathosystems Resource Integration Center (RRID:SCR_004154) | PATRIC | analysis service resource, bioinformatics resource center, data analysis service, data or information resource, database, production service resource, service resource | A Bioinformatics Resource Center bacterial bioinformatics database and analysis resource that provides researchers with an online resource that stores and integrates a variety of data types (e.g. genomics, transcriptomics, protein-protein interactions (PPIs), three-dimensional protein structures and sequence typing data) and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes, currently more than 10 000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. The PATRIC project includes three primary collaborators: the University of Chicago, the University of Manchester, and New City Media. The University of Chicago is providing genome annotations and a PATRIC end-user genome annotation service using their Rapid Annotation using Subsystem Technology (RAST) system. The National Centre for Text Mining (NaCTeM) at the University of Manchester is providing literature-based text mining capability and service. New City Media is providing assistance in website interface development. An FTP server and download tool are available. | genomics, genome, transcriptomics, protein-protein interaction, sequence typing, proteobacteria, brucella, rickettsia, coxiella, coronavirus, calicivirus, lyssavirus, virus, hepatitis a, hepatitis e, pathway, proteome, metabolic pathway, drug, vaccine, diagnostics, FASEB list |
is listed by: OMICtools has parent organization: Virginia Polytechnic Institute and State University; Virginia; USA |
NIAID | PMID:24225323 PMID:17142235 |
Free, Public, Acknowledgement requested | r3d100010142, OMICS_01658, nlx_17476 | http://patricbrc.vbi.vt.edu/portal/portal/patric/Home, https://doi.org/10.17616/R3WS3X | http://patric.vbi.vt.edu/ | SCR_004154 | PathoSystems Resource Integration Center, PATRIC, Pathosystems Resource Integration Center | 2026-09-12 01:00:10 | 1114 | |||
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Gene Weaver Resource Report Resource Website 10+ mentions |
Gene Weaver (RRID:SCR_003009) | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | Freely accessible phenotype-centered database with integrated analysis and visualization tools. It combines diverse data sets from multiple species and experiment types, and allows data sharing across collaborative groups or to public users. It was conceived of as a tool for the integration of biological functions based on the molecular processes that subserved them. From these data, an empirically derived ontology may one day be inferred. Users have found the system valuable for a wide range of applications in the arena of functional genomic data integration. | phenotype, microarray, gene, genome, functional genomics, process, pathway, function, gene set, genomic data integration, analysis, visualization |
is used by: NIF Data Federation is used by: Integrated Datasets is listed by: OMICtools is related to: Integrated Manually Extracted Annotation has parent organization: Jackson Laboratory |
Integrative Neuroscience Initiative on Alcoholism ; NIAAA R01 AA18776; NIAAA U01 AA13499; NIAAA U24 AA13513 |
PMID:22080549 PMID:19733230 |
Free, Freely available | r3d100012464, OMICS_02232, nif-0000-00517 | http://ontologicaldiscovery.org/, https://doi.org/10.17616/R3248T | SCR_003009 | GeneWeaver, GeneWeaver - A system for the integration of functional genomics experiments, Ontological Discovery Environment, GeneWeaver.org | 2026-09-12 01:00:09 | 39 | |||||
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Sequence Tag Alignment and Consensus Knowledgebase Database Resource Report Resource Website |
Sequence Tag Alignment and Consensus Knowledgebase Database (RRID:SCR_002156) | data or information resource, data processing software, data visualization software, database, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The STACKdb is knowledgebase generated by processing EST and mRNA sequences obtained from GenBank through a pipeline consisting of masking, clustering, alignment and variation analysis steps. The STACK project aims to generate a comprehensive representation of the sequence of each of the expressed genes in the human genome by extensive processing of gene fragments to make accurate alignments, highlight diversity and provide a carefully joined set of consensus sequences for each gene. The STACK project is comprised of the STACKdb human gene index, a database of virtual human transcripts, as well as stackPACK, the tools used to create the database. STACKdb is organized into 15 tissue-based categories and one disease category. STACK is a tool for detection and visualization of expressed transcript variation in the context of developmental and pathological states. The data system organizes and reconstructs human transcripts from available public data in the context of expression state. The expression state of a transcript can include developmental state, pathological association, site of expression and isoform of expressed transcript. STACK consensus transcripts are reconstructed from clusters that capture and reflect the growing evidence of transcript diversity. The comprehensive capture of transcript variants is achieved by the use of a novel clustering approach that is tolerant of sub-sequence diversity and does not rely on pairwise alignment. This is in contrast with other gene indexing projects. STACK is generated at least four times a year and represents the exhaustive processing of all publicly available human EST data extracted from GenBank. This processed information can be explored through 15 tissue-specific categories, a disease-related category and a whole-body index | exonic, expressed, expressed sequence tag (est), expression, fragment, gene, alignment, alternative gene, cdna, clone, cluster, developmental, disease, diversity, genome, homo sapiens, human, isoform, knowledgebase, meta-cluster, mrna, pathological, sequence, tissue, transcript, variant, visualization | PMID:11125101 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20946 | SCR_002156 | STACKdb | 2026-09-12 01:00:07 | 0 | ||||||||
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UK Sheep Genome Mapping Project Resource Report Resource Website 1+ mentions |
UK Sheep Genome Mapping Project (RRID:SCR_002272) | data or information resource, database, portal, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The project aims to apply genome mapping research to sheep, utilizing previous research in sheep (in other countries) and in other species (in the UK and abroad) to the benefit of the UK sheep industry. The project itself uses existing breeding structures, knowledge of the sheep genome and experimental resources. It has three main aims: i) To use the Suffolk, Texel and Charollais Sire Referencing Schemes to detect and verify quantitative trait loci (QTLs) for growth and carcass composition traits ii) To investigate candidate genes and/or chromosomal regions for associations with production traits. iii) To investigate approaches for optimizing future genotyping strategies within the sire referencing schemes for practical and cost effective application of marker-assisted selection By using commercial breeding populations for the research, immediate application of beneficial results is possible. Potential benefits include increased genetic progress through marker assisted selection which utilizes the genotype information, correction of possible parentage errors (ultimately leading to additional genetic progress) and opportunities for using marker information for product certification. The project will benefit the UK sheep industry by the use of Marker Assisted Selection (MAS) utilizing QTL or gene variants identified in the project. Additional benefits may arise from parentage verification and correction of errors e.g. misallocation of lamb to ewe. In the longer term, opportunities may exist to use markers for quality control, tracing products to their source. The major advantage of the design of this project is that the results are immediately applicable to the breeding schemes within which the QTLs and/or genes are detected. The time lag in the application of the results that is often seen with experimental populations is minimized. The project requires close involvement with the Sire Reference Schemes, in return for their assistance the results have immediate benefit to animals within these groups. | gene, animal, breed, breeding, chromosomal, chromosome, genome, genotype, genotyping, lamb, map, mapping, marker, population, production, region, sheep, specie, structure, trait | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20995 | SCR_002272 | UKSGMP | 2026-09-12 01:00:08 | 1 | |||||||||
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SoyBase Resource Report Resource Website 500+ mentions |
SoyBase (RRID:SCR_005096) | SoyBase | analysis service resource, controlled vocabulary, data analysis service, data or information resource, data repository, database, ontology, production service resource, service resource, storage service resource | Professionally curated repository for genetics, genomics and related data resources for soybean that contains the most current genetic, physical and genomic sequence maps integrated with qualitative and quantitative traits. SoyBase includes annotated Williams 82 genomic sequence and associated data mining tools. The genetic and sequence views of the soybean chromosomes and the extensive data on traits and phenotypes are extensively interlinked. This allows entry to the database using almost any kind of available information, such as genetic map symbols, soybean gene names or phenotypic traits. The repository maintains controlled vocabularies for soybean growth, development, and traits that are linked to more general plant ontologies. Contributions to SoyBase or the Breeder''s Toolbox are welcome. | soybean, gene, genetic map, genome, data set, trait, phenotype, molecular biology, sequence, chromosome, quantitative trait locus, php, genetics, genomics, legume, bio.tools, FASEB list |
is listed by: 3DVC is listed by: re3data.org is listed by: Debian is listed by: bio.tools has parent organization: Iowa State University; Iowa; USA is parent organization of: Soybean Ontologies is parent organization of: Soy Ontology |
USDA Agricultural Research Service | PMID:20008513 | The community can contribute to this resource | nif-0000-03483, r3d100010846, biotools:soybase | https://bio.tools/soybase, https://doi.org/10.17616/R3S032 | SCR_005096 | SoyBase and the Soybean Breeder''s Toolbox, SoyBase and the Soybean Breeder''s Toolbox: Integrating Genetics and Molecular Biology for Soybean Researchers | 2026-09-12 01:00:10 | 830 | ||||
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SOURCE Resource Report Resource Website 50+ mentions |
SOURCE (RRID:SCR_005799) | SOURCE | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | SOURCE compiles information from several publicly accessible databases, including UniGene, dbEST, UniProt Knowledgebase, GeneMap99, RHdb, GeneCards and LocusLink. GO terms associated with LocusLink entries appear in SOURCE. The mission of SOURCE is to provide a unique scientific resource that pools publicly available data commonly sought after for any clone, GenBank accession number, or gene. SOURCE is specifically designed to facilitate the analysis of large sets of data that biologists can now produce using genome-scale experimental approaches Platform: Online tool | genomic, functional annotation, ontology, gene expression, gene, genome, statistical analysis, bio.tools, FASEB list |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: SMD |
NIGMS ; NCI CA85129-04; NIGMS GM07365 |
PMID:12519986 | Restricted | biotools:source, nlx_149287 | https://login.stanford.edu/idp/profile/SAML2/Redirect/SSO?execution=e1s1, https://bio.tools/source | SCR_005799 | 2026-09-12 01:00:11 | 69 |
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