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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
Aspergillus Genomes
 
Resource Report
Resource Website
Aspergillus Genomes (RRID:SCR_001880) Aspergillus Genomes analysis service resource, data analysis service, data or information resource, database, production service resource, service resource A resource for viewing annotated genes arising from various Aspergillus sequencing and annotation projects, resulting from the merging of Central Aspergillus Data REpository (CADRE) and The Aspergillus Website, which took place in June 2008. The principal role of CADRE is to aid the Aspergillus research community by managing Aspergillus genome data and by providing visualization tools, ranging from relatively simple annotation displays to more complex data integration displays. In contrast, The Aspergillus Website provides a range of information to the medical community (i.e., clinicians, patients and scientists) regarding the genus Aspergillus and the diseases, such as Aspergillosis, that it can cause. CADRE has been implemented using the Ensembl v22 suite. This suite comprises: * a database schema, which has been devised for storing annotated eukaryotic genomes. The schema is implemented with the MySQL relational database management system. * several specialized programming modules for building interfaces (i.e., BioPerl and Ensembl API modules). * a series of programs (i.e., Perl CGI scripts using the API modules) for viewing genomic data within a web browser., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. genome, eukaryotic genome, gene, gene annotation, aspergillosis, aspergillus, pathway, annotation, sequence, metabolic pathway, genomics, clinical, strain, dna, peptide, blast Fungal Research Trust PMID:19039001 THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-02577, r3d100011253 https://doi.org/10.17616/R3005P SCR_001880 2026-09-05 06:24:41 0
SPHINX
 
Resource Report
Resource Website
SPHINX (RRID:SCR_000534) SPHINX analysis service resource, data analysis service, production service resource, service resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Hybrid binning tool that achieves high binning efficiency by utilizing both "compositional" and "similarity" features of the query sequence during the binning process. SPHINX can analyze sequences in metagenomic data sets as rapidly as composition based approaches, but nevertheless has the accuracy and specificity of similarity based algorithms., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. metagenome, taxonomy, sequence, binning is listed by: OMICtools PMID:21030462 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01466 SCR_000534 2026-09-05 06:24:21 0
Ishtar
 
Resource Report
Resource Website
Ishtar (RRID:SCR_000538) software resource A program for designing primer pairs that amplify multiple target sequences using DNA thermodynamics and one class support vector machines. Written in Python. dna, thermodynamics, sequence, primer, pairs, loci, bioinformatics has parent organization: SourceForge Free, Available for download, Freely available, nlx_71525 SCR_000538 2026-09-05 06:24:21 0
Computational Cancer Genomics Group
 
Resource Report
Resource Website
1+ mentions
Computational Cancer Genomics Group (RRID:SCR_000772) data analysis software, data or information resource, data processing software, database, software application, software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. The Computational Cancer Genomics (CCG) group is dedicated to the development of analysis tools and databases relating molecular sequences and biological functions. Sponsors: This group is supported by the Swiss Institute of Bioinformatics (SIB). eukaryotic, expression, function, gene, analyzer, annotation, biological, clustering, computational, data, genome, in vitro, mapping, messengerrna, molecular, mpss, mrna, one-dimensional, organism, promoter, sage, sequence, snp, software, tag, technology, tool, transcription, transcriptome has parent organization: SIB Swiss Institute of Bioinformatics THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-25561 SCR_000772 CCG 2026-09-05 06:24:25 3
Cystic Fibrosis Mutation Database
 
Resource Report
Resource Website
10+ mentions
Cystic Fibrosis Mutation Database (RRID:SCR_000685) CFTR1, CFMDB data or information resource, data repository, database, service resource, storage service resource Collection of mutations in CFTR gene for international cystic fibrosis genetics research community. Provides up to date information about individual mutations in CFTR gene. All known CFTR mutations and sequence variants have been converted to standard nomenclature recommended by Human Genome Variation Society. On line process for submission of new mutations has been added.While they continue to ensure quality of data, they urge international community to give them feedback and suggestions. Clinical information in this database relates only to details of discovery of specific mutations. As part of 2010 upgrade, CFTR1 joined new project called CFTR2 - Clinical and Functional TRanslation of CFTR. Links to CFTR2 for many mutations in CFTR1 will provide up-to-date summaries of genotype-phenotype information from patient registries around the world. Gene, genetic, amino acid, clinical, cystic fibrosis, mutation, phenotype, genotype-phenotype, genotype, dna sequence, mouse, sequence, genetic variation, polymorphism, translation, function, sequence variation, metadata standard, cftr2, FASEB list is related to: CFTR2 Cystic fibrosis Free, Freely available nif-0000-21105, r3d100012093 https://doi.org/10.17616/R38356 SCR_000685 2026-09-05 06:24:24 42
DeNovoGear
 
Resource Report
Resource Website
1+ mentions
DeNovoGear (RRID:SCR_000670) software resource A software for detecting de novo mutations using sequencing data. It utilizes likelihood-based error modeling to reduce the false positive rate of mutative discovery in exome analysis. It also uses fragment information to identify the parental origin of germ-line mutations. de novo, mutation, sequence, dna, rna, error modeling, exome analysis is listed by: OMICtools
has parent organization: SourceForge
has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA
PMID:23975140 Free, Available for download, Freely available OMICS_00083 https://github.com/denovogear/denovogear SCR_000670 2026-09-05 06:24:23 3
MEGA
 
Resource Report
Resource Website
1000+ mentions
MEGA (RRID:SCR_000667) MEGA, MEGA6, MEGA4, MEGA 4, MEGA 11 data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit Software integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses. Used for comparative analysis of DNA and protein sequences to infer molecular evolutionary patterns of genes, genomes, and species over time. MEGA version 4 expands on existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. MEGA version 6 enables inference of timetrees, as it implements RelTime method for estimating divergence times for all branching points in phylogeny. comparative, analysis, DNA, protein, sequence, molecular, evolution, pattern, gene, genome, evolution, FASEB list has parent organization: Pennsylvania State University Burroughs-Wellcome Fund ;
Japan Society for the Promotion of Science ;
NHGRI HG002096;
NHGRI HG006039;
NIGMS R01GM126567;
NIGMS R35GM139504;
NSF ABI 1661218
DOI:10.1093/molbev/msab120
PMID:24132122
PMID:31904846
PMID:22923298
PMID:21546353
PMID:17488738
PMID:15260895
PMID:11751241
PMID:8019868
Free, Available for download, Freely available SCR_023017, nlx_156838 https://www.megasoftware.net/mega4/ SCR_000667 MEGA11, Molecular Evolutionary Genetics Analysis, Molecular Evolutionary Genetics Analysis 6, Molecular Evolutionary Genetics Analysis 4 2026-09-05 06:24:23 2774
Functional Biosciences
 
Resource Report
Resource Website
1+ mentions
Functional Biosciences (RRID:SCR_000943) service resource A service that provides low cost DNA sequencing. They utilize microfluidic technology. dna, sequencing, sequence, gene, genome, microfluidic, technology is listed by: ScienceExchange SciEx_9422 http://www.scienceexchange.com/facilities/functional-biosciences-inc SCR_000943 Functional Biosciences Inc. 2026-09-05 06:24:27 2
GenoViewer
 
Resource Report
Resource Website
GenoViewer (RRID:SCR_001203) GenoViewer software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Open source viewer / browser software for the SAM / BAM format commonly used in the assembly tasks of Next Generation Sequencing data. next-generation sequencing, sequence, mutation, windows, linux, mac os x, genome, browser, sam, bam, fasta, gff, read error, snp, mnp, insertion, deletion is listed by: OMICtools PMID:22359445 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_02146 https://github.com/astrid/GenoViewer SCR_001203 2026-09-05 06:24:31 0
SomaticCall
 
Resource Report
Resource Website
SomaticCall (RRID:SCR_001196) SomaticCall software resource Software program that finds single-base differences (substitutions) between sequence data from tumor and matched normal samples. It is designed to be highly stringent, so as to achieve a low false positive rate. It takes as input a BAM file for each sample, and produces as output a list of differences (somatic mutations). Note: This software package is no longer supported and information on this page is provided for archival purposes only. somatic mutation, substitution, sequence, bam, mutation is listed by: OMICtools
has parent organization: Broad Institute
Tumor, Cancer, Normal OMICS_02155 SCR_001196 2026-09-05 06:24:30 0
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
Structure-function linkage database
 
Resource Report
Resource Website
10+ mentions
Structure-function linkage database (RRID:SCR_001375) SFLD data or information resource, database A database of hierarchical classification of enzymes that relates specific sequence-structure features to specific chemical capabilities. The SFLD classifies evolutionarily related enzymes according to shared chemical functions and maps these shared functions to conserved active site features. The classification is hierarchical, where broader levels encompass more distantly related proteins with fewer shared features. It thus serves as the analysis and archive site for superfamilies targeted by the Enzyme Function Initiative, and is developed by the Babbitt Laboratory in collaboration with the UCSF Resource for Biocomputing, Visualization, and Informatics. The resource also provides a collection of tools and data for investigating sequence-structure-function relationships and hypothesizing function. software, enzyme, structure-function relationship, blast, reaction, superfamily, hidden markov model, sequence alignment, protein similarity network, sequence, structure, function uses: UCSF Chimera
has parent organization: Resource for Biocomputing Visualization and Informatics
NIGMS R01GM60595;
NIGMS P01GM071790;
NIGMS U54GM093342
PMID:18428763
PMID:16489747
Free, Freely available, nlx_152532 SCR_001375 2026-09-05 06:24:34 18
DDBJ Sequence Read Archive
 
Resource Report
Resource Website
50+ mentions
DDBJ Sequence Read Archive (RRID:SCR_001370) DRA data or information resource, data repository, database, service resource, storage service resource Archive database for output data generated by next-generation sequencing machines including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, and others. DRA is a member of the International Nucleotide Sequence Database Collaboration (INSDC) and archiving the data in a close collaboration with NCBI Sequence Read Archive (SRA) and EBI Sequence Read Archive (ERA). Please submit the trace data from conventional capillary sequencers to DDBJ Trace Archive., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. sequence, next-generation sequencing, sequence read, FASEB list is listed by: OMICtools
is affiliated with: INSDC
is related to: NCBI Sequence Read Archive (SRA)
is related to: European Nucleotide Archive (ENA)
is related to: NCBI Sequence Read Archive (SRA)
has parent organization: DNA DataBank of Japan (DDBJ)
Japanese Ministry of Education Culture Sports Science and Technology MEXT PMID:22009675
PMID:21062823
THIS RESOURCE IS NO LONGER IN SERVICE r3d100013696, OMICS_01027, nlx_152515 http://trace.ddbj.nig.ac.jp/dra/ SCR_001370 2026-09-05 06:24:33 95
VIROME
 
Resource Report
Resource Website
10+ mentions
VIROME (RRID:SCR_004362) VIROME analysis service resource, data analysis service, data or information resource, database, production service resource, service resource A web-application designed for scientific exploration of metagenome sequence data collected from viral assemblages occurring within a number of different environmental contexts. The VIROME informatics pipeline focuses on the classification of predicted open-reading frames (ORFs) from viral metagenomes. The portal allows you to submit your viral metagenome to be processed through the VIROME analysis pipeline, and enable you to investigate your data via the VIROME user interface., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. open-reading frame, metagenome, virus, environment, sequence, library, genetic, polymorphism, orfan, environmental sequencing, shotgun metagenomics, viral ecology, function, taxonomy, peptide, blast is listed by: OMICtools
is related to: UniRef
is related to: CAMERA
is related to: Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis
has parent organization: University of Delaware; Delaware; USA
has parent organization: University of Maryland School of Medicine; Maryland; USA
Gordon and Betty Moore Foundation ;
NSF award 0959894
PMID:23407591 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01506 SCR_004362 Viral Informatics Resource for Metagenome Exploration, Viral Informatics Resource for Metagenome Exploration - VIROME 2026-09-05 06:25:18 22
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
ProViDE
 
Resource Report
Resource Website
100+ mentions
ProViDE (RRID:SCR_004709) ProViDE software resource A similarity based binning algorithm that uses a customized set of alignment parameter thresholds / ranges, specifically suited for the accurate taxonomic labelling of viral metagenomic sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. metagenome, taxonomy, sequence, virus is listed by: OMICtools PMID:21544173 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01463 SCR_004709 ProViDE: Program for Viral Diversity Estimation, Program for Viral Diversity Estimation 2026-09-05 06:25:23 279
Repository of molecular brain neoplasia data
 
Resource Report
Resource Website
1+ mentions
Repository of molecular brain neoplasia data (RRID:SCR_004704) REMBRANDT analysis service resource, data analysis service, data or information resource, database, portal, production service resource, service resource, topical portal THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 28,2023. REMBRANDT is a data repository containing diverse types of molecular research and clinical trials data related to brain cancers, including gliomas, along with a wide variety of web-based analysis tools that readily facilitate the understanding of critical correlations among the different data types. REMBRANDT aims to be the access portal for a national molecular, genetic, and clinical database of several thousand primary brain tumors that is fully open and accessible to all investigators (including intramural and extramural researchers), as well as the public at-large. The main focus is to molecularly characterize a large number of adult and pediatric primary brain tumors and to correlate those data with extensive retrospective and prospective clinical data. Specific data types hosted here are gene expression profiles, real time PCR assays, CGH and SNP array information, sequencing data, tissue array results and images, proteomic profiles, and patients'''' response to various treatments. Clinical trials'''' information and protocols are also accessible. The data can be downloaded as raw files containing all the information gathered through the primary experiments or can be mined using the informatics support provided. This comprehensive brain tumor data portal will allow for easy ad hoc querying across multiple domains, thus allowing physician-scientists to make the right decisions during patient treatments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. gene, genetic, cancer, glioma, tumor, clinical genomics, functional genomics, clinical trial, genomics, gene expression, chromosomal aberration, clinical data, clinical, cellular pathway, gene ontology, molecule, brain, neoplasia, brain tumor, adult, pediatric, child, adolescent, gene expression profile, real time pcr assay, cgh array, snp array, sequence, tissue array, image, proteomic profile, treatment, protocol, molecular data, oncology, data mining, copy number array, gene expression array, secretion, kinase, membrane, gene-anomaly, translational research, personalized medicine, data integration, pathway, cell, phenotype is related to: Gene Ontology
is related to: Glioma Molecular Dignostic Initiatives
has parent organization: National Cancer Institute
Glioma, Brain cancer, Brain tumor NCI ;
NINDS
PMID:19208739 THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-00230 SCR_004704 REMBRANDT (Repository of Molecular Brain Neoplasia Data), REMBRANDT - Repository of Molecular Brain Neoplasia Data, REpository for Molecular BRAin Neoplasia DaTa (REMBRANDT) 2026-09-05 06:25:23 2
AFTOL
 
Resource Report
Resource Website
10+ mentions
AFTOL (RRID:SCR_004650) AFTOL biospecimen repository, material storage repository, service resource, storage service resource THIS RESOURCE IS NO LONGER IN SERVICE, documented Jan 13, 2022; To enhance the understanding of the evolution of the Kingdom Fungi, 1500+ species were sampled for eight gene loci across all major fungal clades, plus a subset of taxa for a suite of morphological and ultrastructural characters with resulting data: AFTOL Molecular Database (generated by WASABI - Web Accessible Sequence Analysis for Biological Inference), Blast search the AFTOL Database (generated by WASABI), AFTOL primers (generated by WASABI), AFTOL primers by species (generated by WASABI), AFTOL alignments, and the AFTOL Structural and Biochemical Database. Users may submit samples to the AFTOL project. AFTOL is a collaboration centered around four universities in the United States: Duke University (Francois Lutzoni and Rytas Vilgalys), Clark University (David Hibbett), Oregon State University (Joey Spatafora), and University of Minnesota (David McLaughlin). Participants throughout the world have donated vouchers, taxon samples, and gene sequences. The aim of the project is to reconstruct the fungal tree of life using all available data for eight loci (nuclear ribosomal DNA: LSU, SSU, ITS (including 5.8s, ITS1 and ITS2); RNA polymerase II: RPB1, RPB2; elongation factor 1-alpha; mitochondrial SSU rDNA, and mitochondrial ATP synthase protein subunit 6). A further objective of this study is to summarize and integrate current knowledge regarding fungal subcellular features within this new phylogenetic framework. The name of the bioinformatic package developed for AFTOL is WASABI which provides an efficient communication platform to facilitate the collection and dissemination of molecular data to (and from) the laboratories and participants. All molecular data can be viewed, downloaded, verified, and corrected by the participants of AFTOL. A central goal of the WASABI interface is to establish an automated analysis framework that includes basecalling of newly generated chromatograms, contig assembly, quality verification of sequences (including a local BLAST), sequence alignment, and congruence test. Gene sequences that pass all tests and are finally verified by their authors will undergo automated phylogenetic analysis on a regular schedule. Although all steps are initially carried out noninteractively, the users can verify and correct the results at any step and thus initiate the reanalysis of dependent data. cytology, morphology, phylogeny, ultrastructure, primer, alignment, blast, sequence, taxonomy, structure, biochemical, subcellular, organism-related portal, data analysis service, culture, sporocarp, dna, pcr product, molecular, molecule, gene sequence has parent organization: Oregon State University; Oregon; USA NSF EF-0228671;
NSF 0090301
PMID:17486962
PMID:21652303
The community can contribute to this resource, THIS RESOURCE IS NO LONGER IN SERVICE nlx_64804 SCR_004650 Assembling the Fungal Tree of Life 2026-09-05 06:25:22 24
DiScRIBinATE
 
Resource Report
Resource Website
1+ mentions
DiScRIBinATE (RRID:SCR_004862) DiScRIBinATE software resource Software for accurate taxonomic classification of metagenomic sequences using a similarity based binning method. User needs to perform a similarity search of the input metagenomic sequences (reads) against the nr protein database using BLASTx search. The generated blastx output is then taken as the input by the DiScRIBinATE program. metagenome, classification, sequence is listed by: OMICtools PMID:21106121 Free for academic use, Non-commercial, Commercial use with permission, Acknowledgement requested, Copyright - Tata Consultancy Services OMICS_01453 SCR_004862 DiScRIBinATE: Distance Score Ratio for Improved Binning and Taxonomic Estimation, Distance Score Ratio for Improved Binning and Taxonomic Estimation 2026-09-05 06:25:25 4
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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