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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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KAVIAR Resource Report Resource Website 10+ mentions |
KAVIAR (RRID:SCR_013737) | data or information resource, database | A database containing a compilation of SNVs, indels, and complex variants observed in humans, designed to facilitate testing for the novelty and frequency of observed variants. | SNV, single nucleotide variant, database, indel, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Institute for Systems Biology; Washington; USA |
Inova Translational Medicine Institute | PMID:21965822 | Free, Public | biotools:kaviar | https://bio.tools/kaviar | SCR_013737 | queryable database of known variants, Known VARiants | 2026-02-14 02:06:20 | 17 | |||||
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MobiDB Resource Report Resource Website 100+ mentions |
MobiDB (RRID:SCR_014542) | data or information resource, database | A database of protein disorder and mobility annotations. The database features three levels of annotation: manually curated data (which are extracted from the DisProt database), indirect data, and predicted data. Additional annotations are included from external sources, including UniProt, Pfam, PDB, and STRING. | database, protein disorder, mobility, annotation, intrinsic protein disorder, bio.tools, FASEB list |
uses: UniProt uses: STRING uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) uses: Pfam is listed by: bio.tools is listed by: Debian has parent organization: University of Padua; Padua; Italy |
Available to the research community | biotools:mobidb | https://bio.tools/mobidb | SCR_014542 | 2026-02-14 02:06:51 | 130 | ||||||||
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Research-tested Intervention Programs (RTIPs) Resource Report Resource Website 10+ mentions |
Research-tested Intervention Programs (RTIPs) (RRID:SCR_016042) | RTIPs | data or information resource, database | Database of cancer control interventions and program materials. It is designed to provide program planners and public health practitioners easy and immediate access to research-tested materials. | cancer, control, intervention, prevention, diagnosis, planning, research, program, public, health, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian |
cancer | NCI | Freely available, Public | biotools:rtips | https://bio.tools/rtips | SCR_016042 | Research-tested Intervention Programs | 2026-02-14 02:06:30 | 25 | ||||
|
3D-footprint Resource Report Resource Website |
3D-footprint (RRID:SCR_015713) | data or information resource, database | Database of DNA-binding protein structures that is updated with Protein Data Bank complexes. It provides structure-based binding specificities and sequence logos, classification and clusters of protein-DNA interfaces, and downloads/stats. | dna binding protein structure, protein data bank, sequencing, protein-dna interface, bio.tools |
is listed by: Debian is listed by: bio.tools works with: footprintDB |
CSIC 200720I038 | PMID:19767616 | Freely available, Free for academic use, Tutorial available | biotools:3d-footprint | https://bio.tools/3d-footprint | SCR_015713 | 2026-02-14 02:06:46 | 0 | ||||||
|
ProteomicsDB Resource Report Resource Website 100+ mentions |
ProteomicsDB (RRID:SCR_015562) | data or information resource, database | Database for the identification of the human proteome and its use across the scientific community. Users can browse proteins and chromosomes and contribute to the data repository. | human proteome, human proteomics, proteomics database, human proteomics database, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: ProteomeTools has parent organization: Technical University of Munich; Bavaria; Germany |
PMID:24870543 | The research community can contribute to this resource | r3d100013408, biotools:proteomicsdb | https://bio.tools/proteomicsdb https://doi.org/10.17616/R31NJMU8 |
SCR_015562 | 2026-02-14 02:06:53 | 149 | |||||||
|
Datasets2Tools Resource Report Resource Website 1+ mentions |
Datasets2Tools (RRID:SCR_016174) | data or information resource, database | Database for the discovery and evaluation of biomedical digital objects. It includes a wide variety of enrichment analyses, gene interaction networks, interactive data visualizations, datasets, and computational tools. | biomedical, digital, bioinformatics, dataset, rna seq, computation, microarray, proteomic, bio.tools |
is listed by: bio.tools is listed by: Debian |
Public, Freely available | biotools:datasets2tools | https://bio.tools/datasets2tools | SCR_016174 | 2026-02-14 02:06:46 | 1 | ||||||||
|
TransmiR Resource Report Resource Website 50+ mentions |
TransmiR (RRID:SCR_017499) | data or information resource, database | Collection of transcription factor microRNA regulations. TransmiR v2.0 manually curated TF-miRNA regulations from publications during 2013-2017 and included ChIP-seq-derived TF-miRNA regulation data. | Transcription, factor, miRNA, regulation, manually, curated, TF-miRNA, ChIPseq, derived, TF-miRNA, data, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: Peking University; Beijing; China |
Restricted | biotools:transmir | https://bio.tools/transmir/ | SCR_017499 | TransmiR v2.0 | 2026-02-14 02:06:32 | 90 | |||||||
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Blood Exposome Database Resource Report Resource Website 1+ mentions |
Blood Exposome Database (RRID:SCR_017610) | data or information resource, database | Collection of chemical compounds and associated information that were automatically extracted by text mining content of PubMed and PubChem databases. Unifies chemical lists from metabolomics, systems biology, environmental epidemiology, occupational expossure, toxiology and nutrition fields. | Chemical, compound, collection, extracted, text, mining, PubMed chemical compounds list, PubChem chemical compounds list, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of California at Davis; California; USA |
NIAID U54 AI138370; NIA U19 AG023122; NIEHS U2C ES030158 |
PMID:31557052 | Free, Available for download, Freely available | biotools:blood-exposome-db | https://github.com/barupal/exposome https://bio.tools/blood-exposome-db |
SCR_017610 | The Blood Exposome Database, exposome | 2026-02-14 02:06:48 | 7 | |||||
|
Skylign Resource Report Resource Website 10+ mentions |
Skylign (RRID:SCR_001176) | Skylign | data analysis service, software resource, service resource, production service resource, analysis service resource | A tool for creating logos representing both sequence alignments and profile hidden Markov models. The interactive logos enable scrolling, zooming, and inspection of underlying values. Skylign can avoid sampling bias in sequence alignments by down-weighting redundant sequences and by combining observed counts with informed priors. It also simplifies the representation of gap parameters, and can optionally scale letter heights based on alternate calculations of the conservation of a position. | sequence alignment, profile, logo, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Janelia Research |
PMID:24410852 | Creative Commons Attribution License, v3 Unported | biotools:skylign, OMICS_02182 | https://bio.tools/skylign | SCR_001176 | Skylign - Interactive logos for alignments and profile HMMs | 2026-02-15 09:18:03 | 13 | |||||
|
sim4cc Resource Report Resource Website |
sim4cc (RRID:SCR_001204) | software application, data processing software, software resource, alignment software, image analysis software | Software tool as cross species spliced alignment program.Heuristic sequence alignment tool for comparing cDNA sequence with genomic sequence containing homolog of gene in another species. | Cross species spliced alignment, unix, sequence alignment, cdna sequence, genomic sequence, homolog, gene, splice, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Johns Hopkins University; Maryland; USA |
NSF CLS20163A; Sloan Research Fellowship ; NLM R01 LM006845 |
PMID:19429899 | Free, Available for download, Freely available | biotools:sim4cc, OMICS_02145 | https://bio.tools/sim4cc | SCR_001204 | 2026-02-15 09:18:04 | 0 | ||||||
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bsseq Resource Report Resource Website 1+ mentions |
bsseq (RRID:SCR_001072) | software application, sequence analysis software, data processing software, software resource, data analysis software | R package with tools for analyzing and visualizing bisulfite sequencing data. | bisulfite sequencing, analyze, r, sequence analysis software, data analysis software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_01847, biotools:bsseq | https://bio.tools/bsseq | SCR_001072 | bsseq - Analyze manage and store bisulfite sequencing data | 2026-02-15 09:18:02 | 8 | |||||||
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SplitSeek Resource Report Resource Website 1+ mentions |
SplitSeek (RRID:SCR_001012) | software application, sequence analysis software, data processing software, software resource, data analysis software | THIS RESOURCE IS NO LONGER IN SERVICE, documented September 20, 2016. A program for de novo prediction of splice junctions in RNA-seq data. | bioinformatics alignment, sequence analysis software, de novo, prediction, rna seq, rna, splice junction, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:20236510 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:splitseek, OMICS_01253 | https://bio.tools/splitseek | http://www.uppmax.uu.se/software/splitseek | SCR_001012 | 2026-02-15 09:18:01 | 1 | ||||||
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AutoAssemblyD Resource Report Resource Website |
AutoAssemblyD (RRID:SCR_001087) | software application, sequence analysis software, data processing software, software resource, data analysis software | Software which performs local and remote genome assembly by several assemblers based on an XML Template which can replace the large command lines required by most assemblers. | genome, genome assembly, xml, sequence analysis software, local genome assembly, remote genome assembly, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:24143057 | Free, Available for download, Freely available | biotools:autoassemblyd, OMICS_00874 | https://bio.tools/autoassemblyd | SCR_001087 | 2026-02-15 09:18:02 | 0 | |||||||
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UNAFold Resource Report Resource Website 100+ mentions |
UNAFold (RRID:SCR_001360) | software application, data processing software, data analysis software, software resource | Software package for nucleic acid folding and hybridization prediction. It has capabilities to predict folding for single-stranded RNA or DNA through a combination of free energy minimization, partition function calculations and stochastic sampling. The program runs on Unix and Linux platforms as well as Mac OS X and Windows. | software, nucleic acid, folding, hybridization, prediction, rna, dna, stochastic sampling, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University at Albany; New York; USA |
Free, Available for download, Freely available | biotools:unafold, nif-0000-07753 | http://mfold.rna.albany.edu/ | SCR_001360 | The UNAFold Web Server, UNAFold Web Server | 2026-02-15 09:18:05 | 304 | |||||||
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Enrichr Resource Report Resource Website 1000+ mentions |
Enrichr (RRID:SCR_001575) | Enrichr | software application, data analysis service, software resource, service resource, production service resource, analysis service resource | A web-based gene list enrichment analysis tool that provides various types of visualization summaries of collective functions of gene lists. It includes new gene-set libraries, an alternative approach to rank enriched terms, and various interactive visualization approaches to display enrichment results using the JavaScript library, Data Driven Documents (D3). The software can also be embedded into any tool that performs gene list analysis. System-wide profiling of genes and proteins in mammalian cells produce lists of differentially expressed genes / proteins that need to be further analyzed for their collective functions in order to extract new knowledge. Once unbiased lists of genes or proteins are generated from such experiments, these lists are used as input for computing enrichment with existing lists created from prior knowledge organized into gene-set libraries. | bed, gene, software as a service, rna-seq, analyze, protein, function, gene list, visualization, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
PMID:23586463 | Free, Freely available | biotools:enrichr, SciRes_000171 | https://bio.tools/enrichr | SCR_001575 | 2026-02-15 09:18:08 | 4351 | ||||||
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An Integrated Multiple Structure Visualization and Multiple Sequence Alignment Application Resource Report Resource Website |
An Integrated Multiple Structure Visualization and Multiple Sequence Alignment Application (RRID:SCR_001646) | software application, data visualization software, data processing software, software resource, rendering software, data analysis software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Friend is a bioinformatics application designed for simultaneous analysis and visualization of multiple structures and sequences of proteins and/or DNA/RNA. The application provides basic functionalities such as: structure visualization with different rendering and coloring, sequence alignment, and simple phylogeny analysis, along with a number of extended features to perform more complex analyses of sequence structure relationships, including: structural alignment of proteins, investigation of specific interaction motifs, studies of protein-protein and protein-DNA interactions, and protein super-families. Friend is also useful for the functional annotation of proteins, protein modeling, and protein folding studies. Friend provides three levels of usage; 1) an extensive GUI for a scientist with no programming experience, 2) a command line interface for scripting for a scientist with some programming experience, and 3) the ability to extend Friend with user written libraries for an experienced programmer. The application is linked and communicates with local and remote sequence and structure databases. | alignment, analysis, bioinformatics, database, dna, interaction, motif, phylogeny, protein, rna, scientist, sequence, structure, super-family, visualization, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Northeastern University; Massachusetts; USA |
PMID:16076889 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:friend, nif-0000-10149 | https://bio.tools/friend | SCR_001646 | FRIEND | 2026-02-15 09:18:08 | 0 | ||||||
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Prediction of Amyloid Structure Aggregation Resource Report Resource Website 100+ mentions |
Prediction of Amyloid Structure Aggregation (RRID:SCR_001768) | PASTA | data analysis service, software resource, web application, service resource, production service resource, analysis service resource | Online interface that utilizes an algorithm to predict the most aggregation-prone portions and the corresponding beta-strand inter-molecular pairing for a given input sequence. Users can paste the sequence into the interface and output the appropriate sequence. | protein aggregation, sequence, dna, rna, amyloid structure, protein analysis, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Padua; Padua; Italy |
Padova University Progetto di Ateneo CPDA121890; Italian Ministry for University and Research FIRB Futuro in Ricerca RBFR08ZSXY; |
PMID:24848016 | Free, Freely available | biotools:pasta, OMICS_03861 | https://bio.tools/pasta | SCR_001768 | PASTA 2.0, Prediction of amyloid structure aggregation | 2026-02-15 09:18:10 | 177 | ||||
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MEME Suite - Motif-based sequence analysis tools Resource Report Resource Website 1000+ mentions |
MEME Suite - Motif-based sequence analysis tools (RRID:SCR_001783) | MEME Suite | software application, source code, data analysis service, data processing software, software resource, database, service resource, production service resource, data or information resource, analysis service resource, data analysis software | Suite of motif-based sequence analysis tools to discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences; search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN; compare a motif to all motifs in a database of motifs; associate motifs with Gene Ontology terms via their putative target genes, and analyze motif enrichment using SpaMo or CentriMo. Source code, binaries and a web server are freely available for noncommercial use. | gene ontology, motif, comparative genomics, dna regulatory motif, dna sequence, dna, gene, transcription factor, genome, protein, analysis, function analysis, comparison, cluster, enrichment analysis, sequence analysis, bio.tools, FASEB list |
lists: DREME is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Glam2 is related to: ANNOgesic is related to: memesuite-lite has parent organization: National Biomedical Computation Resource is parent organization of: GOMO - Gene Ontology for Motifs |
NCRR R01 RR021692 | PMID:19458158 DOI:10.1093/nar/gkl198 |
Free, Freely available | nif-0000-10298, biotools:meme_suite, OMICS_08103 | https://bio.tools/meme_suite | http://meme.sdsc.edu/meme4_6_1/intro.html, http://meme.nbcr.net/meme/, https://sources.debian.org/src/meme/ | SCR_001783 | The MEME Suite | 2026-02-15 09:18:10 | 2091 | |||
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Gene Index Project Resource Report Resource Website 100+ mentions |
Gene Index Project (RRID:SCR_002148) | TGI, DFCI TGI | portal, database, software resource, data or information resource, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on August 19,2019.The goal of The Gene Index Project is to use the available Expressed Sequence Transcript (EST) and gene sequences, along with the reference genomes wherever available, to provide an inventory of likely genes and their variants and to annotate these with information regarding the functional roles played by these genes and their products. The promise of genome projects has been a complete catalog of genes in a wide range of organisms. While genome projects have been successful in providing reference genome sequences, the problem of finding genes and their variants in genomic sequence remains an ongoing challenge. TGI has created an inventory that contains genes and their variants together with description. In addition, this resource is attempting to use these catalogs to find links between genes and pathways in different species and to provide lists of features within completed genomes that can aid in the understanding of how gene expression is regulated. DATABASES *Eukaryotic Gene Orthologues (formerly known as TOGA - TIGR Orthologous Gene Alignment): Eukaryotic Gene Orthologues (EGO) at DFGI are generated by pair-wise comparison between the Tentative Consensus (TC) sequences that comprise the Dana Farber Gene Indices from individual organisms. The reciprocal pairs of the best match were clustered into individual groups and multiple sequence alignments were displayed for each group. *GeneChip Oncology Database (GCOD):Cancer gene expression database is a collection of publicly available microarray expression data on Affymetrix GeneChip Arrays related to human cancers. Currently only datasets with available raw data (Affymetrix .CEL files) are processed. All processed datasets were subjected to extensive manual curation, uniform processing and consistent quality control. You can browse the experiments in our collection, perform statistical analysis, and download processed data; or to search gene expression profiles using Entrez gene symbol, Unigene ID, or Affymetrix probeset ID. *Gene Indices: As of July 1, 2008, there are 111 publicly available gene indices. They are separated into 4 categories for better organization and easier access. Animal: 41, Plant: 45, Protist: 15, Fungal: 10 *Genomic Maps: Human, mouse, rat, chicken, drosophila melanogaster, zebrafish, mosquito, caenorhabditis elegans, Arabidopsis thaliana, rice, yeast, fission yeast Dana-Farber Cancer Institute (DFCI) Gene Indices Software Tools: *TGI Clustering tools (TGICL): a software system for fast clustering of large EST datasets. *GICL: this package contains the scripts and all the necessary pre-compiled binaries for 32bit Linux systems. *clview: an assembly file viewer. *SeqClean:a script for automated trimming and validation of ESTs or other DNA sequences by screening for various contaminants, low quality and low-complexity sequences. *cdbfasta/cdbyank: fast indexing/retrieval of fasta records from flat file databases. *DAS/XML Genomic Viewer The Genomic viewer borrows modules from http://www.biodas.org (lstein (at) cshl.org) & http://webreference.com. | functional, gene, genome, index, organism, pathway, product, role, sequence, species, transcript, variant, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Dana-Farber Cancer Institute |
DOE DBI-0552416 | PMID:7566098 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:tigr_gene_indices, nif-0000-20942 | https://bio.tools/tigr_gene_indices | SCR_002148 | DFCI Gene Index Project, Gene Index Project, DFCI | 2026-02-15 09:18:15 | 129 | ||||
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SHARCGS Resource Report Resource Website 1+ mentions |
SHARCGS (RRID:SCR_002026) | software application, sequence analysis software, data processing software, software resource, data analysis software | Software package for a DNA assembly program designed for de novo assembly of 25-40mer input fragments and deep sequence coverage. | dna, assembly, de novo, rna, sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Max Planck Institute for Molecular Genetics; Berlin; Germany |
PMID:17908823 | Free, Available for download, Freely available | OMICS_00029, biotools:sharcgs | https://bio.tools/sharcgs | SCR_002026 | SHort read Assembler based on Robust Contig extension for Genome Sequencing (SHARCGS), SHARCGS - SHort read Assembler based on Robust Contig extension for Genome Sequencing, SHort read Assembler based on Robust Contig extension for Genome Sequencing | 2026-02-15 09:18:13 | 4 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant 2U24DK097771-09.
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