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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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GenoMiner Resource Report Resource Website |
GenoMiner (RRID:SCR_001202) | GenoMiner | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A next generation sequencing data analysis computer for biologists with or without IT background. It has an easy to-use graphical interface to analyze sequencing data in with only 15 clicks. A range of standard, add-on and custom applications help analyze and visualize data generated by Next Generation Sequencing machines. These are installed on each GenoMiner by default: * Reference assembly * De novo assembly * ChiP-Seq * BLAST * Hybrid de novo assembly * Hybrid reference assembly Add-on applications: * Quality assesment * RNA-Seq * Copy Number Variation (CNV) * Multiple Sequence Alignment * miRNA-Seq * Variant Calling | next-generation sequencing, reference assembly, de novo assembly, chip-seq, blast, hybrid de novo assembly, hybrid reference assembly, genome, computer, hardware, instrument, equipment | is listed by: OMICtools | PMID:16267081 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02149 | http://www.astridbio.com/genominer.html | SCR_001202 | GenoMiner: Genome Analyzer | 2026-09-05 06:24:31 | 0 | |||||
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PeakAnalyzer Resource Report Resource Website 1+ mentions |
PeakAnalyzer (RRID:SCR_001194) | PeakAnalyzer | software resource | A set of standalone software programs for the automated processing of any genomic loci, with an emphasis on datasets consisting of ChIP-derived signal peaks. The software is able to identify individual binding / modification sites from enrichment loci, retrieve peak region sequences for motif discovery, and integrate experimental data with different classes of annotated elements throughout the genome. PeakAnalyzer requires a peak file and a feature annotation file in BED or GTF format. Complete annotation files for the current builds of the human (HG19) and mouse (MM9) genomes are provided with the software distribution. | genome, chip, signal peak, binding site, modification site, enrichment loci, peak region, sequence, motif, chip-seq, chip-chip, c++, java, linux, mac os x, windows, bed, gtf, annotation, r, high-throughput sequencing, chromatin binding, modification loci, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: European Bioinformatics Institute |
PMID:20691053 | Free, Available for download, Freely available | biotools:peakanalyzer, OMICS_02156 | https://bio.tools/peakanalyzer | SCR_001194 | 2026-09-05 06:24:30 | 3 | ||||||
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Breakway Resource Report Resource Website |
Breakway (RRID:SCR_001180) | Breakway | software resource | A suite of software programs that take aligned genomic data and report structural variation breakpoints. Features include: * Takes in BAM formatted input, the current standard for genomic alignments. * Compatible with standard output from major alignment algorithms such as BFAST, BWA, MAQ, et cetera. * Capable of analyzing data from any major platform--Solexa, SOLiD, 454, et cetera. * Empirically identifies structural variation breakpoints. * Highly specific analysis generates very few false positives. * Includes a suite of downstream tools for annotating identified breakpoints and reducing false positives. | genome, structural variation, breakpoint |
is listed by: OMICtools has parent organization: SourceForge has parent organization: University of California at Los Angeles; California; USA |
PMID:20126413 | Free, Available for download, Freely available | OMICS_02176 | SCR_001180 | Breakway: Identify Structural Variations in Genomic Data | 2026-09-05 06:24:30 | 0 | ||||||
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ChIP-seq Resource Report Resource Website 5000+ mentions |
ChIP-seq (RRID:SCR_001237) | ChIP-seq | data analysis software, data processing software, software application, software resource, software toolkit | Set of software modules for performing common ChIP-seq data analysis tasks across the whole genome, including positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-poor regions. The tools are designed to be simple, fast and highly modular. Each program carries out a well-defined data processing procedure that can potentially fit into a pipeline framework. ChIP-Seq is also freely available on a Web interface. | high-throughput sequencing, chromatin immuno precipitation, chip-seq, genome, c |
is listed by: OMICtools has parent organization: SourceForge has parent organization: Ecole Polytechnique Federale de Lausanne; Lausanne; Switzerland has parent organization: SIB Swiss Institute of Bioinformatics |
PMID:27863463 | Free, Available for download, Freely available | OMICS_02103 | https://epd.expasy.org/chipseq/, https://chip-seq.sourceforge.net/ | SCR_001237 | ChIP-seq - Tools for the analysis of ChIP-seq data | 2026-09-05 06:24:31 | 8035 | |||||
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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 | 2026-09-05 06:25:19 | 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 | 2026-09-05 06:25:18 | 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 | 2026-09-05 06:25:18 | 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 | 2026-09-05 06:25:23 | 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 | 2026-09-05 06:25:22 | 9170 | |||||
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GeneDB Lmajor Resource Report Resource Website 1+ mentions |
GeneDB Lmajor (RRID:SCR_004613) | GeneDB_Lmajor, GeneDB Lmajor, GeneDB L. major, | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Database of the most recent sequence updates and annotations for the L. major genome. New annotations are constantly being added to keep up with published manuscripts and feedback from the Trypanosomatid research community. You may search by Protein Length, Molecular Mass, Gene Type, Date, Location, Protein Targeting, Transmembrane Helices, Product, GO, EC, Pfam ID, Curation and Comments, and Dbxrefs. BLAST and other tools are available. Leishmania species cause a spectrum of human diseases in tropical and subtropical regions of the world. We have sequenced the 36 chromosomes of the 32.8-megabase haploid genome of Leishmania major (Friedlin strain) and predict 911 RNA genes, 39 pseudogenes, and 8272 protein-coding genes, of which 36% can be ascribed a putative function. These include genes involved in host-pathogen interactions, such as proteolytic enzymes, and extensive machinery for synthesis of complex surface glycoconjugates. The Pathogen Genomics group at the Wellcome Trust Sanger Institute played a major role in sequencing the genome of Leishmania major (see Ivens et al.) Details of the centres involved and which chromosomes they sequenced, are given. The sequence data were obtained by adopting several parallel approaches, including complete cosmid sequencing, whole chromosome shotguns and/or BAC sequencing/skimming. The Leishmania parasite is an intracellular pathogen of the immune system targeting macrophages and dendritic cells. The disease Leishmaniasis affects the populations of 88 counties worldwide with symptoms ranging from disfiguring cutaneous and muco-cutaneous lesions that can cause widespread destruction of mucous membranes to visceral disease affecting the haemopoetic organs. In collaboration with GeneDB, the EuPathDB genomic sequence data and annotations are regularly deposited on TriTrypDB where they can be integrated with other datasets and queried using customized queries. | genome, gene, rna gene, rna, pseudogene, protein-coding, function, host-pathogen interaction, interaction, proteolytic enzyme, glycoconjugate, sequence annotation |
is used by: NIF Data Federation is related to: AmiGO is related to: TriTrypDB has parent organization: GeneDB |
Wellcome Trust | PMID:16020728 | nlx_60997 | SCR_004613 | Leishmania major strain Friedlin, Leishmania major strain Friedlin homepage on GeneDB, GeneDB Leishmania major, Leishmania major strain Friedlin on GeneDB | 2026-09-05 06:25:22 | 7 | ||||||
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Nucleotide database Resource Report Resource Website 100+ mentions |
Nucleotide database (RRID:SCR_004630) | nucest | data or information resource, data repository, database, service resource, storage service resource | Nucleotide database as collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery. | Genome, gene, transcript sequence data, GenBank, RefSeq, TPA, PDB, gold standard |
is listed by: re3data.org is related to: BMAP cDNA Resources is related to: GenBank has parent organization: NCBI |
PMID:8401577 | Free, Freely available | SCR_016578, nlx_62971 | SCR_004630 | 2026-09-05 06:25:22 | 167 | |||||||
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LMAT Resource Report Resource Website 10+ mentions |
LMAT (RRID:SCR_004646) | LMAT | software resource | Open-source software tool to assign taxonomic labels to as many reads as possible in very large metagenomic datasets and report the taxonomic profile of the input sample. The quick "single pass" analysis of every read allows read binning to support additional more computationally expensive analysis such as metagenomic assembly or sensitive database searches on targeted subsets of reads. | c++, metagenomic, metagenomic classification, genome, virus, taxonomy, database, reference genome |
is listed by: OMICtools has parent organization: Lawrence Livermore National Laboratory has parent organization: SourceForge |
PMID:23828782 | Open unspecified license | OMICS_02285 | SCR_004646 | Livermore Metagenomics Analysis Toolkit | 2026-09-05 06:25:22 | 15 | ||||||
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MetaPhyler Resource Report Resource Website 10+ mentions |
MetaPhyler (RRID:SCR_004848) | software resource | A taxonomic classifier for metagenomic shotgun reads, which uses phylogenetic marker genes as a taxonomic reference. The classifier, based on BLAST, uses different thresholds (automatically learned from the reference database) for each combination of taxonomic rank, reference gene, and sequence length. The reference database includes marker genes from all complete genomes, several draft genomes and the NCBI nr protein database. | metagenome, classification, sequence, taxonomy, genome, microbiome, bio.tools |
is listed by: OMICtools is listed by: Human Microbiome Project is listed by: Debian is listed by: bio.tools has parent organization: University of Maryland; Maryland; USA |
PMID:21989143 | Acknowledgement requested, Available for download | OMICS_01455, biotools:metaphyler | https://bio.tools/metaphyler | SCR_004848 | MetaPhyler - Estimating Bacterial Composition from Metagenomic Sequences | 2026-09-05 06:25:25 | 11 | ||||||
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NCBI BLAST Resource Report Resource Website 10000+ mentions |
NCBI BLAST (RRID:SCR_004870) | BLAST | data access protocol, data analysis software, data processing software, sequence analysis software, software application, software resource, web service | Web search tool to find regions of similarity between biological sequences. Program compares nucleotide or protein sequences to sequence databases and calculates statistical significance. Used for identifying homologous sequences. | genome, similarity, sequence, nucleotide, protein, gene, data, bio.tools |
is used by: MITE-Tracker is used by: Cello2Go is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: G-BLASTN is related to: genBlastA has parent organization: NCBI is required by: RelocaTE works with: Whole Genome Shotgun (WGS) Project works with: BLASTClust works with: MOLE-BLAST works with: Genotyping |
National Library of Medicine | PMID:16845079 PMID:18440982 |
Free, Freely available, Tutorial available | OMICS_01436, nlx_84530, biotools:blast | http://blast.ncbi.nlm.nih.gov, https://bio.tools/blast, https://sources.debian.org/src/ncbi-blast+/ | SCR_004870 | NCBI Basic Local Alignment Search Tool, NCBI BLAST, Basic Local Alignment Search Tool, BLAST | 2026-09-05 06:25:25 | 17718 | ||||
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PANTHER Resource Report Resource Website 5000+ mentions |
PANTHER (RRID:SCR_004869) | PANTHER | analysis service resource, controlled vocabulary, data analysis service, data or information resource, database, ontology, production service resource, service resource | System that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in absence of direct experimental evidence. Orthologs view is curated orthology relationships between genes for human, mouse, rat, fish, worm, and fly., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | hidden markov model, human, mouse, genome, protein, gene, function, pathway, ortholog, phylogenetic tree, gene ortholog, protein family, gene function, evolution, data set, molecular function, biological process, cellular component, transcript, FASEB list |
is used by: NIF Data Federation is used by: YPED is used by: EMBRYS is related to: Gene Ontology is related to: Pathway Commons is related to: KOBAS has parent organization: University of Southern California; Los Angeles; USA is parent organization of: PANTHER Evolutionary analysis of coding SNPs |
NIGMS GM081084 | PMID:23193289 PMID:20015972 PMID:12952881 |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015893, nlx_84521 | SCR_004869 | PANTHER Classification System, Protein ANalysis THrough Evolutionary Relationships Classification System, Protein ANalysis THrough Evolutionary Relationships, PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System | 2026-09-05 06:25:25 | 8830 | |||||
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PRISM - Pair Read Informed Split Mapper Resource Report Resource Website 1+ mentions |
PRISM - Pair Read Informed Split Mapper (RRID:SCR_004812) | PRISM (Pair Read Informed Split Mapper) | software resource | Software for split read (reads which span across a structrual variant -- SV ) mapping and SV calling from the mapping result. It is able to detect small insertions and abitrary size deletions, inversions and tandom duplications with the direction of discordant read pairs. PRISM_CTX is a tool for detecting inter-chromosome trans-location events. | structural variant, split read mapping, insertion, deletion, inversion, tandom duplication, discordant read pair, chromosome, trans-location event, duplication, breakpoint, genome |
is listed by: OMICtools has parent organization: University of Toronto; Ontario; Canada |
PMID:22851530 | Free, Public | OMICS_02288 | SCR_004812 | PRISM (Pair Read Informed Split Mapper), Pair Read Informed Split Mapper | 2026-09-05 06:25:24 | 7 | ||||||
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Database of Genomic Variants Archive (DGVa) Resource Report Resource Website 100+ mentions |
Database of Genomic Variants Archive (DGVa) (RRID:SCR_004896) | DGVa | data or information resource, data repository, database, service resource, storage service resource | Public repository that accepts direct submissions and provides archiving, accessioning and distribution of publicly available genomic structural variants, in all species. Variants are accessioned at the study and sample level, granting stable identifiers that can be used in publications. DGVa data is integrated with other EBI resources, including comprehensive EBI search and Ensembl genome browser. Exchanges data with companion database, dbVar, at National Center for Biotechnology Information.NOTE: since 2019 DGVa doesn't accept submissions. Please send the data for submission to European Variation Archive (EVA). | genome, dna, gene, expression, genetics, mapping, structural, variant, gold standard |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is related to: dbVar is related to: ISCA Consortium is related to: Database of Genomic Variants is related to: Ensembl Variation has parent organization: European Bioinformatics Institute |
PMID:23193291 PMID:24174537 |
Free, Freely available | nlx_86626, r3d100010814 | https://doi.org/10.17616/R3HK7Z | http://www.ebi.ac.uk/dgva/page.php, http://www.ebi.ac.uk/dgva/ | SCR_004896 | , DGVarchive, DGVa, Database of Genomic Variants Archive | 2026-09-05 06:25:26 | 211 | ||||
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Eurexpress Resource Report Resource Website 1+ mentions |
Eurexpress (RRID:SCR_005093) | Eurexpress | atlas, data or information resource, database, expression atlas, image collection | Genome transcriptome atlas by RNA in situ hybridization on sagittal sections of developing mouse at embryonic day 14.5. Consists of searchable database of annotated images that can be interactively viewed. Anatomy based expression profiles for coding genes and microRNAs, tissue specific genes. Expression data generated by using human and murine tissue arrays. | Genome, transcriptome, atlas, RNA, in situ, hybrydization, sagittal, section, developing, mouse, embryo, expression, gene |
is listed by: GUDMAP Ontology is listed by: NIDDK Information Network (dkNET) is related to: EMAGE Gene Expression Database is related to: aGEM has parent organization: Telethon Institute of Genetics and Medicine; Naples; Italy |
Association pour la Recherche sur le Cancer ; European Union ; Ingenio 2010 MEuropean Union ; Max Planck Society ; MRC ; Swiss National Science Foundation ; Telethon Foundation ; VI Framework |
PMID:21267068 | nif-0000-00243 | http://www.eurexpress.org/ee/databases/anatomy/treeFrames.jsp, http://www.eurexpress.org/ee/ | SCR_005093 | Eurexpress atlas, Transcriptome Atlas Database for Mouse Embryo | 2026-09-05 06:25:29 | 3 | |||||
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SMART Resource Report Resource Website 5000+ mentions |
SMART (RRID:SCR_005026) | SMART | analysis service resource, data access protocol, data analysis service, data or information resource, database, production service resource, service resource, software resource, web service | Software tool for identification and annotation of genetically mobile domains and analysis of domain architectures. | extracellular, gene, genetic, genetically, genome, architecture, chromatin, domain, mobile, phyletic, protein, proteome, signaling, structure, taxonomic, tertiary, bio.tools, FASEB list |
is used by: Mutation Annotation and Genomic Interpretation is listed by: bio.tools is listed by: Debian is related to: Eukaryotic Linear Motif is related to: Conserved Domain Database is related to: GOTaxExplorer has parent organization: EMBL - Bork Group |
European Union | PMID:18978020 PMID:16381859 PMID:14681379 PMID:10592234 PMID:9847187 PMID:9600884 |
Free, Freely available | nif-0000-03471, biotools:smart | http://smart.embl-heidelberg.de/, https://bio.tools/smart | SCR_005026 | Simple Modular Architecture Research Tool | 2026-09-05 06:25:28 | 8432 | ||||
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AnnTools Resource Report Resource Website 1+ mentions |
AnnTools (RRID:SCR_005170) | AnnTools | software resource | Software tool for annotating single nucleotide substitutions (SNP/SNV), small insertions/deletions (indels), and copy number variations (CNV) calls generated from sequencing and microarray data. Only human genome build 37/hg19 can be annotated at this time. | single nucleotide substitution, snp, snv, indel, copy number variation, sequencing, microarray, linux, unix, mac osx, python, mysql, genome annotation, genome, annotation |
is listed by: OMICtools has parent organization: SourceForge |
BSD License | OMICS_00166 | SCR_005170 | 2026-09-05 06:25:30 | 4 |
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