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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Clippers Resource Report Resource Website 1+ mentions |
Clippers (RRID:SCR_005256) | Clippers | software resource | A software program designed to identify long deletions of a genome as well as the RNA splicings using long Illumina reads. Currently, Clippers is implemented for long reads Illumina, ex: 75bp or 100bp, allowing mismatches and a single deletion/splicing. Clippers is a sister tool of PerM, our short reads aligner. Users are strongly suggested to use PerM to initially mapped reads and identify the deletion/splicing with the initially unmapped reads. We plan to extend it to ABI SOLiD reads in the near future. Clippers outputs gap-alignments in SAM format. You can use SAMtools or other program to interpret the deletion/splicing. The input files are a reference in fasta format and the reads is in fasta or fastq format. | long deletion, genome, rna splicing, illumina, deletion |
is listed by: OMICtools is related to: PerM has parent organization: Google Code has parent organization: University of Southern California; Los Angeles; USA |
PMID:19675096 | GNU General Public License, v2, Acknowledgement requested | OMICS_00311 | SCR_005256 | clippers - Deletion Identification Program using Periodic Spaced Seed | 2026-09-19 12:50:50 | 7 | ||||||
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AGE Resource Report Resource Website 1+ mentions |
AGE (RRID:SCR_005253) | AGE | software resource | A tool that implements an algorithm for optimal alignment of sequences with Structural Variations (SVs). | genome |
is listed by: OMICtools has parent organization: Yale University; Connecticut; USA |
OMICS_00305 | SCR_005253 | 2026-09-19 12:50:50 | 3 | |||||||||
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SkateBase Resource Report Resource Website 10+ mentions |
SkateBase (RRID:SCR_005302) | SkateBase | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Portal supporting the North East Bioinformatics Collaborative''s project to sequence the genome of the Little Skate. Provided is a clearinghouse for Little Skate Genome Project and other publicly available Skate and Ray (Batoidea) genome data, and tools for data visualization and analysis. Little Skate Genome Project The little skate (Leucoraja erinacea) is a chondrichthyan (cartilaginous) fish native to the east coast of North America. Elasmobranchs (Skates, Rays, and Sharks) exhibit many fundamental vertebrate characteristics, including a neural crest, jaws and teeth, an adaptive immune system, and a pressurized circulatory system. These characteristics have been exploited to promote understanding about human physiology, immunology, stem cell biology, toxicology, neurobiology and regeneration. The development of standardized experimental protocols in elasmobranchs such as L. erinacea and the spiny dogfish shark (Squalus acanthias) has further positioned these organisms as important biomedical and developmental models. Despite this distinction, the only reported chondrichthyan genome is the low coverage (1.4x) draft genome of the elephant shark (Callorhinchus milii). To close the evolutionary gaps in available elasmobranch genome sequence data, and generate critical genomic resources for future biomedical study, the genome of L. erinacea is being sequenced by the North East Bioinformatics Collaborative (NEBC). As close evolutionary relatives, the little skate sequence will facilitate studies that employ dogfish shark and other elasmobranchs as model organisms. Skate tools include the SkateBLAST and the Skate Genome Browsers: Little Skate Mitochondrion, Thorny Skate Mitochondrion, and Ocellate Spot Skate Mitochondrion. | little skate, leucoraja erinacea, sequence, genome, mitochondrion, thorny skate, ocellate spot skate, FASEB list |
has parent organization: North East Cyberinfrastructure Consortium has parent organization: University of Delaware; Delaware; USA has parent organization: University of Delaware Skate Genome Project |
NIGMS 3P20GM103446-12S1 | nlx_144350 | SCR_005302 | 2026-09-19 12:50:51 | 40 | ||||||||
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inGAP Resource Report Resource Website 10+ mentions |
inGAP (RRID:SCR_005261) | inGAP | software resource | Software mining pipeline guided by a Bayesian principle to detect single nucleotide polymorphisms, insertion and deletions by comparing high-throughput pyrosequencing reads with a reference genome of related organisms. This pipeline is extended to identify and visualize large-size structural variations, including insertions, deletions, inversions and translocations. | structural variation, genome, next-generation sequence, genome analysis, alignment, single nucleotide polymorphism, insertion, deletion, indel, inversion, translocation, windows, linux, macos/x, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Fudan University; Shanghai; China has parent organization: Chinese Academy of Sciences; Beijing; China |
OMICS_00319, biotools:ingap | https://bio.tools/ingap | SCR_005261 | inGAP-sv, inGAP-sv: structural variation detection and visualization, integrative next-generation genome analysis pipeline | 2026-09-19 12:50:50 | 29 | |||||||
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PEMer Resource Report Resource Website 1+ mentions |
PEMer (RRID:SCR_005263) | software resource | Software package as computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Package is composed of three modules, PEMer workflow, SV-Simulation and BreakDB. PEMer workflow is a sensitive software for detecting SVs from paired-end sequence reads. SV-Simulation randomly introduces SVs into a given genome and generates simulated paired-end reads from novel genome. | structural variation, genome, next-generation sequencing, bio.tools, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: BreakDB has parent organization: European Molecular Biology Laboratory |
PMID:19236709 | biotools:pemer, OMICS_00320 | https://bio.tools/pemer, https://bio.tools/pemer | SCR_005263 | Paired-End Mapper | 2026-09-19 12:50:50 | 7 | |||||||
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Gene Wiki Resource Report Resource Website 1+ mentions |
Gene Wiki (RRID:SCR_005317) | Gene Wiki | data or information resource, narrative resource, wiki | The Gene Wiki is a project that facilitates transferring information on human genes to Wikipedia article stubs with the goal of promoting collaboration and expansion of the articles. Number of gene articles The human genome contains an estimated 20,00025,000 protein-coding genes. The goal of the Gene Wiki project is to create seed articles for every notable human gene, that is, every gene whose function has been assigned in the peer-reviewed scientific literature. Approximately half of human genes have assigned function, therefore the total number of articles seeded by the Gene Wiki project would be expected to be in the range of 10,000 - 15,000. To date, approximately 10,271 articles have been created or augmented to include Gene Wiki project content. Expansion Once seed articles have been established, the hope and expectation is that these will be annotated and expanded by editors ranging in experience from the lay audience to students to professionals and academics. Proteins encoded by genes The majority of genes encode proteins hence understanding the function of a gene generally requires understanding of the function of the corresponding protein. In addition to including basic information about the gene, the project therefore also includes information about the protein encoded by the gene. Stubs for the Gene Wiki project are created by a bot and contain links to the following primary gene/protein databases * HUGO Gene Nomenclature Committee official gene name * Entrez Gene database * OMIM (Mendelian Inheritance in Man) database that catalogues all the known diseases with a genetic component * Amigo Gene Ontology * HomoloGene gene homologs in other species * SymAtlasRNA gene expression pattern in tissues * Protein Data Bank 3D structure of protein encoded by the gene * Uniprot (universal protein resource) a central repository of protein data | gene, genome, human, annotation | has parent organization: Wikipedia | PMID:18613750 | nlx_144371 | SCR_005317 | GeneWiki | 2026-09-19 12:50:51 | 3 | |||||||
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GNUMAP Resource Report Resource Website 1+ mentions |
GNUMAP (RRID:SCR_005482) | GNUMAP | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 3rd,2023. A software program designed to accurately map sequence data obtained from next-generation sequencing machines (specifically that of Solexa/Illumina) back to a genome of any size. By using the posterior probability of mapping a given read to a specific genomic loation, we are able to account for repetitive reads by distributing them across several regions in the genome. In addition, the output of the program is created in such a way that it can be easily viewed through other free and readily- available programs. Several benchmark data sets were created with spiked-in duplicate regions, and GNUMAP was able to more accurately account for these duplicate regions. | next-generation sequencing, genome, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Brigham Young University; Utah; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00664, biotools:gnumap | https://bio.tools/gnumap | SCR_005482 | Genomic Next-generation Universal MAPper | 2026-09-19 12:50:54 | 7 | ||||||
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CUSHAW2-GPU Resource Report Resource Website |
CUSHAW2-GPU (RRID:SCR_005480) | CUSHAW2-GPU | software resource | Software program (based on CUSHAW2) designed and optimized for Kepler-based GPUs, but still workable on earlier-generation Fermi-based ones. | c++, genome, alignment |
is listed by: OMICtools is related to: CUSHAW has parent organization: SourceForge |
Apache License | OMICS_00659 | SCR_005480 | 2026-09-19 12:50:54 | 0 | ||||||||
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CGAT Resource Report Resource Website 1+ mentions |
CGAT (RRID:SCR_005550) | CGAT | software resource | A comparative genome analysis tool for detailed comparison of closely related bacterial-sized genomes. It visualizes precomputed pairwise genome alignments on both dotplot and alignment viewers. Users can add information on this alignment, such as existence of tandem repeats or interspersed repetitive sequences and changes in codon usage bias, to facilitate interpretation of the observed genomic changes. Besides visualization functionalities, it also provides a general framework to process genome-scale alignments using various existing alignment programs. CGAT employs a client-server architecture, which consists of AlignmentViewer (client; a Java application) and DataServer (a set of Perl scripts). The DataServer package contains data construction scripts and CGI scripts and the AlignmentViewer program visualizes the alignment data obtained from the server thorough the HTTP protocol. | genome, alignment, visualizing, evolution, dotplot |
is listed by: OMICtools has parent organization: National Institute for Basic Biology; Okazaki; Japan |
PMID:17062155 | OMICS_00930 | SCR_005550 | CGAT - A Comparative Genome Analysis Tool, Comparative Genome Analysis Tool | 2026-09-19 12:50:55 | 3 | |||||||
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CUSHAW Resource Report Resource Website 1+ mentions |
CUSHAW (RRID:SCR_005479) | CUSHAW | software resource | Software package for next-generation sequencing read alignment that is fast and parallel gapped read alignment to large genomes, such as the human genome. | next-generation sequencing, read alignment, genome, alignment |
is listed by: OMICtools is related to: CUSHAW2-GPU has parent organization: Johannes Gutenberg University Mainz; Rhineland-Palatinate; Germany has parent organization: SourceForge |
PMID:22576173 PMID:24466273 |
OMICS_00658 | SCR_005479 | CUSHAW2, CUSHAW3 | 2026-09-19 12:50:54 | 2 | |||||||
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Manatee Resource Report Resource Website 50+ mentions |
Manatee (RRID:SCR_005685) | Manatee | software resource | Manatee is a web-based gene evaluation and genome annotation tool; Manatee can store and view annotation for prokaryotic and eukaryotic genomes. The Manatee interface allows biologists to quickly identify genes and make high quality functional assignments, such as GO classifications, using search data, paralogous families, and annotation suggestions generated from automated analysis. Manatee can be downloaded and installed to run under the CGI area of a web server, such as Apache. Platform: Online tool, Linux compatible, Solaris | gene, genome, annotation, ontology or annotation browser, ontology or annotation editor |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: J. Craig Venter Institute has parent organization: University of Maryland School of Medicine; Maryland; USA has parent organization: SourceForge |
Open unspecified license - Free for academic use | nlx_149128 | SCR_005685 | 2026-09-19 12:50:57 | 64 | ||||||||
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Sybil Resource Report Resource Website 10+ mentions |
Sybil (RRID:SCR_005593) | Sybil | data or information resource, database, software resource | A web-based software package for comparative genomics. | comparative genomics, genome, synteny, protein cluster, protein, gene, genomic region, synteny gradient, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:22121156 | OMICS_00945, biotools:sybil | https://bio.tools/sybil | SCR_005593 | Sybil: Web-based software for comparative genomics | 2026-09-19 12:50:56 | 37 | ||||||
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LookSeq Resource Report Resource Website 1+ mentions |
LookSeq (RRID:SCR_005625) | LookSeq | software resource | A web-based application for alignment visualization, browsing and analysis of genome sequence data. | alignment, visualization, browsing, analysis, genome, sequence |
is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
OMICS_00886 | SCR_005625 | 2026-09-19 12:50:56 | 5 | |||||||||
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Human Adenovirus Type Classification Resource Report Resource Website 100+ mentions |
Human Adenovirus Type Classification (RRID:SCR_005753) | HAdV Type Classification | analysis service resource, knowledge environment, production service resource, service resource | The Human Adenovirus Type Classification coordinates the naming of candidate new types, prior to manuscript submission for peer review. This resource contains a method of submitting candidate HAdV, criteria for a new HAdV type, and a Serotyping tool, which displays all potential types corresponding to the query serotype entered by a user. The criteria are based on discussions at the International Adenovirus Meeting (Dobog��k, Hungary; 26-30 April, 2009) and the NIH Human Adenovirus Working Group Workshop (Bethesda, MD. USA; 3 February 2011), which are summarized in a Letter to the Editor. | hadv, human adenovirus, adenovirus, classification, serotyping, genotyping, genome, nucleotide sequence, human adenovirus working group, serotype | has parent organization: George Mason University; Virginia; USA | Adenovirus | nlx_149215 | SCR_005753 | 2026-09-19 12:50:59 | 153 | ||||||||
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CLIPZ Resource Report Resource Website 10+ mentions |
CLIPZ (RRID:SCR_005755) | CLIPZ | 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 August 20,2019.Database and analysis environment for experimentally determined binding sites of RNA-binding proteins. It supports the automatic functional annotation of short reads resulting primarily from crosslinking and immunoprecipitation experiments (CLIP) performed with RNA-binding proteins in order to identify the binding sites of these proteins. The functional annotation could be also applied to short reads resulting from other types of experiments such as mRNA-Seq, Digital Gene Expression, small RNA cloning, etc. The platform enables visualization and mining of individual data sets as well as analysis involving multiple experimental data sets. The platform can support collaborative projects involving multiple users and groups of users as well as public and private datasets. | rna-binding protein, binding site, protein, functional annotation, cross-linking and immunoprecipitation, short read, mrna-seq, digital gene expression, small rna cloning, visualization, mining, analysis, post-transcriptional regulatory element, genome, transcript, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SIB Swiss Institute of Bioinformatics has parent organization: University of Basel; Basel; Switzerland |
PMID:21087992 | THIS RESOURCE IS NO LONGER IN SERVICE. | OMICS_02256, biotools:clipz | https://bio.tools/clipz | SCR_005755 | 2026-09-19 12:50:59 | 20 | ||||||
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SCPD - Saccharomyces cerevisiae promoter database Resource Report Resource Website 10+ mentions |
SCPD - Saccharomyces cerevisiae promoter database (RRID:SCR_004412) | SCPD | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | A promoter database of Saccharomyces cerevisiae. Users can explore the promoter regions of ~6000 genes and ORFs in yeast genome, annotate putative regulatory sites of all genes and ORFs, locate intergenic regions, and retrieve sequence of the promoter region. In regards to regulatory elements and transcription factors, users can provide information on transcriptionally related genes, browse matrix and consensus sequences, view the correlation between elements, observe binding affinity and expression, and look at genomewise distribution. SCPD also provides some simple but useful tools for promoter sequence analysis. Gene, consensus and matrix records may be submitted. | promoter, gene, genome, orf, transcription factor binding site, transcriptional start site, transcription factor |
is listed by: OMICtools has parent organization: Cold Spring Harbor Laboratory |
PMID:10487868 | OMICS_01867, nif-0000-03445 | SCR_004412 | SCPD - The Promoter Database of Saccharomyces cerevisiae | 2026-09-19 12:50:37 | 20 | |||||||
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SO Resource Report Resource Website 10+ mentions |
SO (RRID:SCR_004374) | SO | controlled vocabulary, data or information resource, ontology | A collaborative ontology for the definition of sequence features used in biological sequence annotation. SO was initially developed by the Gene Ontology Consortium. Contributors to SO include the GMOD community, model organism database groups such as WormBase, FlyBase, Mouse Genome Informatics group, and institutes such as the Sanger Institute and the EBI. Input to SO is welcomed from the sequence annotation community. The OBO revision is available here: http://sourceforge.net/p/song/svn/HEAD/tree/ SO includes different kinds of features which can be located on the sequence. Biological features are those which are defined by their disposition to be involved in a biological process. Biomaterial features are those which are intended for use in an experiment such as aptamer and PCR_product. There are also experimental features which are the result of an experiment. SO also provides a rich set of attributes to describe these features such as polycistronic and maternally imprinted. The Sequence Ontologies use the OBO flat file format specification version 1.2, developed by the Gene Ontology Consortium. The ontology is also available in OWL from Open Biomedical Ontologies. This is updated nightly and may be slightly out of sync with the current obo file. An OWL version of the ontology is also available. The resolvable URI for the current version of SO is http://purl.obolibrary.org/obo/so.owl. | annotation, sequence, biological sequence, sequence variation, genome, genome annotation, owl, FASEB list |
is listed by: BioPortal is related to: ASOoViR is related to: VAGrENT has parent organization: OBO has parent organization: Gene Ontology |
NHGRI HG02273 | PMID:20796305 PMID:20226267 PMID:18629179 PMID:15892872 |
The community can contribute to this resource | nlx_38918 | SCR_004374 | Sequence Ontology Project, Sequence Types and Features Ontology, Sequence Ontology | 2026-09-19 12:50:36 | 46 | |||||
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Velvet-SC Resource Report Resource Website 1+ mentions |
Velvet-SC (RRID:SCR_004377) | Velvet SC | data analysis software, data processing software, sequence analysis software, software application, software resource | Software package for short read data from single cells that improves assembly through use of progressively increasing coverage cutoff. Used for single cell Illumina sequences, allows variable coverage datasets to be utilized with assembly of E. coli and S. aureus single cell reads. Assembles single cell genome of uncultivated SAR324 clade of Deltaproteobacteria. | genome, single, cell, short, read, assembly |
is listed by: OMICtools is related to: Velvet has parent organization: University of California at San Diego; California; USA |
NCRR P41 RR024851; NHGRI R01 HG003647; Sloan Foundation |
PMID:21926975 | Free, Available for download, Freely available | OMICS_01504 | SCR_004377 | Velvet Single Cell | 2026-09-19 12:50:37 | 5 | |||||
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RAIphy Resource Report Resource Website 1+ mentions |
RAIphy (RRID:SCR_004720) | RAIphy | software resource | A semi-supervised metagenomic fragment classification software program that utilizes the genome signatures to characterize the DNA sequences and taxonomic classification is based on an information theoretic measure referred as Relative Abundance Index (RAI). A DNA sequence of unknown source is classified and taxonomically labeled based on the phylogenetic profiles of the previously sequenced genomes. The profiles are iteratively updated using the unknown DNA sequences and the classification results. After a few cycles, the metagenome is classified into operational taxonomic units. | classification, metagenome, phylogenetic profile, genome, taxonomic classification, dna sequence, relative abundance index |
is listed by: OMICtools has parent organization: University of Nebraska; Nebraska; USA |
PMID:21281493 | OMICS_01464 | SCR_004720 | 2026-09-19 12:50:41 | 3 | ||||||||
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TAIR Resource Report Resource Website 5000+ mentions |
TAIR (RRID:SCR_004618) | TAIR, AGI LocusCode | data or information resource, database | Database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. Data available includes the complete genome sequence along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community. Gene product function data is updated every two weeks from the latest published research literature and community data submissions. Gene structures are updated 1-2 times per year using computational and manual methods as well as community submissions of new and updated genes. TAIR also provides extensive linkouts from data pages to other Arabidopsis resources. The data can be searched, viewed and analyzed. Datasets can also be downloaded. Pages on news, job postings, conference announcements, Arabidopsis lab protocols, and useful links are provided. | genetic, molecular biology, gene, genome, structure, product, metabolism, gene expression, dna, seed stock, genome map, genetic marker, physical marker, genome sequence, gene product, blast, experimental protocol, gold standard |
is used by: NIF Data Federation is listed by: OMICtools is listed by: re3data.org is listed by: DataCite is related to: AmiGO is related to: Saskatoon Arabidopsis T-DNA mutant population SK Collection is related to: CLENCH has parent organization: Carnegie Institution for Science is parent organization of: TAIR Keyword Browser is parent organization of: PubSearch |
NSF DBI-0850219; corporate and nonprofit organizations |
PMID:22140109 PMID:17986450 PMID:12444417 PMID:12519987 PMID:18287693 |
r3d100010185, nlx_61477, OMICS_01662 | https://doi.org/10.17616/R3QW21 | SCR_004618 | AGI LocusCode, The Arabidopsis Information Resource | 2026-09-19 12:50:40 | 9170 |
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