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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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GenePattern Resource Report Resource Website 1000+ mentions |
GenePattern (RRID:SCR_003201) | GenePattern | software application, software resource, data analysis software, data processing software | A powerful genomic analysis platform that provides access to hundreds of tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research. | gene expression, analysis, genomic, pattern, proteomics, silico, snp, workflow, analysis pipeline, flow cytometry, rna-seq, data processing, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite is affiliated with: GenePattern Notebook is related to: TIGRESS has parent organization: Broad Institute |
NCI ; NIGMS |
PMID:16642009 | Free, Freely available | biotools:genepattern, OMICS_01855, nif-0000-30654 | https://bio.tools/genepattern | SCR_003201 | 2026-07-28 09:40:44 | 1078 | |||||
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Cell Image Library (CIL) Resource Report Resource Website 10+ mentions |
Cell Image Library (CIL) (RRID:SCR_003510) | CIL | service resource, data or information resource, data repository, image repository, database, storage service resource | Freely accessible, public repository of vetted and annotated microscopic images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes. Explore by Cell Process, Cell Component, Cell Type or Organism. The Cell includes images acquired from historical and modern collections, publications, and by recruitment. | microscopic image repository, microscopic video repository, cell animation repository, bio.tools |
is used by: NIF Data Federation is recommended by: National Library of Medicine 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 listed by: bio.tools is listed by: Debian is related to: Cell Centered Database is related to: Cell Centered Database is related to: OME-TIFF Format is related to: Integrated Manually Extracted Annotation has parent organization: American Society for Cell Biology has parent organization: University of California; San Diego;National Center for Microscopy and Imaging Research - NCMIR has parent organization: University of California at San Diego; California; USA is parent organization of: Biological Imaging Methods Ontology |
NIGMS RC2 GM092708 | PMID:34218671 PMID:34218673 |
Free, Freely available | biotools:cellimagelibrary, nif-0000-37639, r3d100011601 | http://www.cellimagelibrary.org/pages/about, https://bio.tools/cellimagelibrary, https://doi.org/10.17616/R3N92J | SCR_003510 | Cell Image Library. CIL, Cell Image Library (CIL) | 2026-07-28 09:40:45 | 19 | ||||
|
Proteomics Identifications (PRIDE) Resource Report Resource Website 500+ mentions |
Proteomics Identifications (PRIDE) (RRID:SCR_003411) | PRIDE | service resource, data or information resource, data repository, database, storage service resource | Centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence. Originally it was developed to provide a common data exchange format and repository to support proteomics literature publications. This remit has grown with PRIDE, with the hope that PRIDE will provide a reference set of tissue-based identifications for use by the community. The future development of PRIDE has become closely linked to HUPO PSI. PRIDE encourages and welcomes direct user submissions of protein and peptide identification data to be published in peer-reviewed publications. Users may Browse public datasets, use PRIDE BioMart for custom queries, or download the data directly from the FTP site. PRIDE has been developed through a collaboration of the EMBL-EBI, Ghent University in Belgium, and the University of Manchester. | proteomics, protein, peptide, mass spectrometry, annotation, standard, spectra, protein-protein interaction, amino acid, amino acid sequence, post-translational modification, biomart, bio.tools |
is used by: ProteomeXchange is used by: BioSample Database at EBI is recommended by: NIDDK Information Network (dkNET) is listed by: Biositemaps is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: HUPO Proteomics Standards Initiative is related to: ProteomeXchange has parent organization: European Bioinformatics Institute |
Wellcome Trust WT085949MA; European Union FP7 LSHG-CT-2006-036814; European Union FP7 260558; European Union FP7 262067; European Union FP7 202272; BBSRC BB/I024204/1 |
PMID:23203882 PMID:19662629 |
Free, Available for download, Freely available | nif-0000-03336, biotools:pride, r3d100011515 | https://www.ebi.ac.uk/pride/archive/, https://bio.tools/pride, https://doi.org/10.17616/R3F330 | SCR_003411 | PRoteomics IDEntifications database, PRIDE Archive - proteomics data repository, PRIDE Archive, PRIDE, Proteomics Identifications, Proteomics Identifications (PRIDE), PRoteomics IDEntifications database (PRIDE) | 2026-07-28 09:40:42 | 642 | ||||
|
Reactome Resource Report Resource Website 1000+ mentions |
Reactome (RRID:SCR_003485) | service resource, data or information resource, data analysis service, database, production service resource, analysis service resource | Collection of pathways and pathway annotations. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways (signaling, innate and acquired immune function, transcriptional regulation, translation, apoptosis and classical intermediary metabolism) . Provides website to navigate pathway knowledge and a suite of data analysis tools to support the pathway-based analysis of complex experimental and computational data sets. | pathway, interaction, reaction, nucleic acid, protein, complex, small molecule, signaling pathway, immune function, transcriptional regulation, translation, apoptosis, metabolism, ortholog, visualization, protein-protein interaction, web service, book, biomart, gold standard, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: DisGeNET is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: WikiPathways is related to: Pathway Commons is related to: ConsensusPathDB is related to: FlyMine is related to: AmiGO is related to: PSICQUIC Registry is related to: Integrated Molecular Interaction Database is related to: NCBI BioSystems Database is related to: MOPED - Model Organism Protein Expression Database is related to: KOBAS is related to: PSICQUIC Registry is related to: Pathway Interaction Database is related to: hiPathDB - human integrated Pathway DB with facile visualization is related to: Algal Functional Annotation Tool has parent organization: Ontario Institute for Cancer Research has parent organization: Cold Spring Harbor Laboratory has parent organization: European Bioinformatics Institute has parent organization: New York University School of Medicine; New York; USA works with: PathwayMatcher |
Ontario Research Fund ; European Molecular Biology Laboratory ; NHGRI P41 HG003751; European Union FP6 ENFIN LSHG-CT-2005-518254; NIGMS GM080223; NIGMS R01 GM100039 |
PMID:21082427 PMID:21067998 |
Open source, Public, Freely available | r3d100010285, nif-0000-03390, biotools:reactome | https://bio.tools/reactome, https://doi.org/10.17616/R3V59P | SCR_003485 | Reactome Functional Interaction Network | 2026-07-28 09:40:48 | 4282 | |||||
|
L-Measure Resource Report Resource Website 10+ mentions |
L-Measure (RRID:SCR_003487) | LM | software application, service resource, software resource, data processing software, image processing software, image analysis software | A freely available software tool available for the Windows and Linux platform, as well as the Online version Applet, for the analysis, comparison and search of digital reconstructions of neuronal morphologies. For the quantitative characterization of neuronal morphology, LM computes a large number of neuroanatomical parameters from 3D digital reconstruction files starting from and combining a set of core metrics. After more than six years of development and use in the neuroscience community, LM enables the execution of commonly adopted analyses as well as of more advanced functions, including: (i) extraction of basic morphological parameters, (ii) computation of frequency distributions, (iii) measurements from user-specified subregions of the neuronal arbors, (iv) statistical comparison between two groups of cells and (v) filtered selections and searches from collections of neurons based on any Boolean combination of the available morphometric measures. These functionalities are easily accessed and deployed through a user-friendly graphical interface and typically execute within few minutes on a set of 20 neurons. The tool is available for either online use on any Java-enabled browser and platform or may be downloaded for local execution under Windows and Linux. | neuronal morphology, neuroinformatics, branching analysis, digital reconstruction, analysis, comparison, bio.tools |
is listed by: 3DVC is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools has parent organization: Computational Neuroanatomy Group |
Human Brain Project ; NINDS R01 NS39600 |
PMID:18451794 | Public | nif-0000-00003, biotools:l-measure | http://www.nitrc.org/projects/lmeasure, https://bio.tools/l-measure | SCR_003487 | 2026-07-28 09:40:44 | 30 | |||||
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GO2MSIG Resource Report Resource Website 1+ mentions |
GO2MSIG (RRID:SCR_018359) | data or information resource, data set |
THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 24, 2020. Software tool as automated Gene Ontology based multi species gene set generator for gene set enrichment analysis. Used to generate gene sets required for Gene Set Enrichment Analysis for almost any organism for which GO term association data exists. Gene set collections can be automatically created for wide variety of species. |
bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Broad Institute |
PMID:24884810 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:go2msig | https://bio.tools/go2msig | http://www.go2msig.org/cgi-bin/go2msig.cgi | SCR_018359 | 2026-07-27 09:35:51 | 4 | ||||||
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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 analysis software, rendering software, software resource, data processing software, data visualization 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 | 2026-07-28 09:40:21 | 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 | service resource, web application, data analysis service, software 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 | 2026-07-28 09:40:24 | 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, service resource, data analysis software, data or information resource, data analysis service, database, data processing software, software resource, source code, production service resource, analysis service resource | 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 | 2026-07-28 09:40:24 | 2091 | |||
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SHARCGS Resource Report Resource Website 1+ mentions |
SHARCGS (RRID:SCR_002026) | software application, data analysis software, sequence analysis software, software resource, data processing 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 | 2026-07-28 09:40:31 | 4 | ||||||
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SHORTY Resource Report Resource Website 1+ mentions |
SHORTY (RRID:SCR_002048) | software application, data analysis software, sequence analysis software, software resource, data processing software | Software for targeted de novo assembly of microreads with mate pair information and sequencing errors. | sequencing, dna, de novo, microreads, assembler, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:19208115 | Free, Available for download, Freely available | biotools:shorty, OMICS_00030 | https://bio.tools/shorty | SCR_002048 | 2026-07-28 09:40:19 | 3 | |||||||
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ASPGD Resource Report Resource Website 100+ mentions |
ASPGD (RRID:SCR_002047) | ASPGD, ASPGD LOCUS, ASPGD REF | service resource, data or information resource, data repository, database, storage service resource | Database of genetic and molecular biological information about the filamentous fungi of the genus Aspergillus including information about genes and proteins of Aspergillus nidulans and Aspergillus fumigatus; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; gene, protein, and chromosome sequence information; tools for analysis and comparison of sequences; and links to literature information; as well as a multispecies comparative genomics browser tool (Sybil) for exploration of orthology and synteny across multiple sequenced Sgenus species. Also available are Gene Ontology (GO) and community resources. Based on the Candida Genome Database, the Aspergillus Genome Database is a resource for genomic sequence data and gene and protein information for Aspergilli. Among its many species, the genus contains an excellent model organism (A. nidulans, or its teleomorph Emericella nidulans), an important pathogen of the immunocompromised (A. fumigatus), an agriculturally important toxin producer (A. flavus), and two species used in industrial processes (A. niger and A. oryzae). Search options allow you to: *Search AspGD database using keywords. *Find chromosomal features that match specific properties or annotations. *Find AspGD web pages using keywords located on the page. *Find information on one gene from many databases. *Search for keywords related to a phenotype (e.g., conidiation), an allele (such as veA1), or an experimental condition (e.g., light). Analysis and Tools allow you to: *Find similarities between a sequence of interest and Aspergillus DNA or protein sequences. *Display and analyze an Aspergillus sequence (or other sequence) in many ways. *Navigate the chromosomes set. View nucleotide and protein sequence. *Find short DNA/protein sequence matches in Aspergillus. *Design sequencing and PCR primers for Aspergillus or other input sequences. *Display the restriction map for a Aspergillus or other input sequence. *Find similarities between a sequence of interest and fungal nucleotide or protein sequences. AspGD welcomes data submissions. | function, gene, gene name, annotation, aspergillus, aspergillus nidulans, chromosome, community, dna, genome, genomic, localization, orthology, phenotype, protein, protein-coding genes, s. cerevisiae, sequence, allele, data analysis service, bio.tools, FASEB list |
is used by: NIF Data Federation is listed by: bio.tools is listed by: Debian is related to: Candida Genome Database is related to: AmiGO has parent organization: Stanford University School of Medicine; California; USA has parent organization: Broad Institute |
NIAID R01 AI077599 | PMID:19773420 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-12244, biotools:aspgd | http://www.aspergillusgenome.org/, https://bio.tools/aspgd | SCR_002047 | Aspergillus Genome Database, ASPGD REF, ASPGD LOCUS | 2026-07-28 09:40:31 | 212 | ||||
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Pathway Commons Resource Report Resource Website 10+ mentions |
Pathway Commons (RRID:SCR_002103) | PC | data or information resource, database, data access protocol, software resource, web service | Database of publicly available pathways from multiple organisms and multiple sources represented in a common language. Pathways include biochemical reactions, complex assembly, transport and catalysis events, and physical interactions involving proteins, DNA, RNA, small molecules and complexes. Pathways were downloaded directly from source databases. Each source pathway database has been created differently, some by manual extraction of pathway information from the literature and some by computational prediction. Pathway Commons provides a filtering mechanism to allow the user to view only chosen subsets of information, such as only the manually curated subset. The quality of Pathway Commons pathways is dependent on the quality of the pathways from source databases. Pathway Commons aims to collect and integrate all public pathway data available in standard formats. It currently contains data from nine databases with over 1,668 pathways, 442,182 interactions,414 organisms and will be continually expanded and updated. (April 2013) | biological pathway, pathway, molecule, biopax, standard exchange format, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: cPath is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: IntAct is related to: Reactome is related to: MINT is related to: HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism is related to: Cancer Cell Map is related to: HPRD - Human Protein Reference Database is related to: Integrated Molecular Interaction Database is related to: Pathway Interaction Database is related to: CHEBI is related to: UniProt is related to: PANTHER is related to: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit has parent organization: University of Toronto; Ontario; Canada |
NHGRI P41HG004118; NIGMS 2R01GM070743-06; NIGMS 1T32 GM083937; Cancer Biomedical Informatics Grid |
PMID:21071392 | Free, Freely available | nif-0000-20884, r3d100012731, biotools:PathwayCommons_web_service_API | https://bio.tools/PathwayCommons_web_service_API | SCR_002103 | 2026-07-28 09:40:20 | 14 | |||||
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SAMTOOLS Resource Report Resource Website 10000+ mentions |
SAMTOOLS (RRID:SCR_002105) | SAMtools | software application, data analysis software, sequence analysis software, software resource, data processing software, software toolkit | Original SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data. | Samtools, BCFtools, HTSlib, next generation sequencing, nucleotide alignments, sequence variant, genomic, c, perl, read, alignment, nucleotide, sequence, data, process, sam, bam, cram, vcf, bcf, bio.tools |
is used by: deFuse is used by: Short Read Sequence Typing for Bacterial Pathogens is used by: ROSE is used by: Fcirc is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: SNVer is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Platypus is related to: shovill is related to: pysam has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom is parent organization of: SAMtools/BCFtools is required by: RelocaTE is required by: Wessim is required by: SL-quant is required by: smMIPfil |
Wellcome Trust ; NHGRI U54 HG002750 |
PMID:19505943 PMID:21903627 DOI:10.1093/bioinformatics/btp352 |
Free, Available for download, Freely available | SCR_018682, biotools:samtools, OMICS_01074, nlx_154607, OMICS_00090 | https://github.com/samtools/samtools, https://github.com/samtools/htslib, https://bio.tools/samtools, https://sources.debian.org/src/samtools/ | http://samtools.sourceforge.net/ | SCR_002105 | samtools, Samtools, Sequence Alignment Map TOOLS, SAMtools, SAM tools | 2026-07-28 09:40:33 | 30156 | |||
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Gene Index Project Resource Report Resource Website 100+ mentions |
Gene Index Project (RRID:SCR_002148) | TGI, DFCI TGI | data or information resource, database, software resource, topical portal, 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 | 2026-07-28 09:40:34 | 129 | ||||
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Fiji Resource Report Resource Website 10000+ mentions |
Fiji (RRID:SCR_002285) | Fiji | software application, source code, software resource, data processing software, image processing software | Software package as distribution of ImageJ and ImageJ2 together with Java, Java3D and plugins organized into coherent menu structure. Used to assist research in life sciences. | imaging, microscopy, windows, linux, java, mac osx, bio.tools |
uses: Fiji/ImageJ is used by: MuscleJ is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: ImageJ is related to: SynapseLocator is related to: Golddigger is related to: Analyze Spheroid Cell Invasion In 3D Matrix has parent organization: Max Planck Institute of Molecular Cell Biology and Genetics; Dresden; Germany has plug in: BioVoxxel Toolbox has plug in: imctools has plug in: Big Data Processor has plug in: Sholl Analysis has plug in: SAIBR has plug in: TWOMBLI |
PMID:22743772 | Free, Available for download, Freely available, Acknowledgement requested | SciRes_000137, biotools:Fiji | https://github.com/fiji/fiji, https://bio.tools/Fiji | SCR_002285 | Fiji is just ImageJ | 2026-07-28 09:40:23 | 37202 | |||||
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Blood Group Antigen Gene Mutation Database Resource Report Resource Website |
Blood Group Antigen Gene Mutation Database (RRID:SCR_002297) | BGMUT | service resource, data or information resource, data repository, database, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 23, 2019.BGMUT was database that provided publicly accessible platform for DNA sequences and curated set of blood mutation information. Data Archive are available at ftp://ftp.ncbi.nlm.nih.gov/pub/mhc/rbc/Final Archive. | blood, gene, genetic, allele, allelic, alteration, antigen, blood group, human, mutation, genetic variation, non-human animal, orthologous gene, orthologue, phenotype, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: NCBI dbRBC has parent organization: Albert Einstein College of Medicine; New York; USA has parent organization: Roswell Park Comprehensive Cancer Center has parent organization: Medical University of Graz; Graz; Austria has parent organization: Human Genome Variation Society |
Albert Einstein College of Medicine; New York; USA ; David Opochinsky/Blumenfeld Family Fund ; NIH |
PMID:22084196 | THIS RESOURCE IS NO LONGER IN SERVICE. | nif-0000-21064, biotools:bgmut | https://bio.tools/bgmut | http://www.bioc.aecom.yu.edu/bgmut/index.htm, http://www.ncbi.nlm.nih.gov/projects/gv/rbc/xslcgi.fcgi?cmd=bgmut | SCR_002297 | Blood Group Antigen Gene Mutation Database (BGMUT), BGMUT - Blood Group Antigen Gene Mutation Database | 2026-07-28 09:40:23 | 0 | |||
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DNA DataBank of Japan (DDBJ) Resource Report Resource Website 500+ mentions |
DNA DataBank of Japan (DDBJ) (RRID:SCR_002359) | DDBJ | service resource, data or information resource, data repository, database, storage service resource | Maintains and provides archival, retrieval and analytical resources for biological information. Central DDBJ resource consists of public, open-access nucleotide sequence databases including raw sequence reads, assembly information and functional annotation. Database content is exchanged with EBI and NCBI within the framework of the International Nucleotide Sequence Database Collaboration (INSDC). In 2011, DDBJ launched two new resources: DDBJ Omics Archive and BioProject. DOR is archival database of functional genomics data generated by microarray and highly parallel new generation sequencers. Data are exchanged between the ArrayExpress at EBI and DOR in the common MAGE-TAB format. BioProject provides organizational framework to access metadata about research projects and data from projects that are deposited into different databases. | nucleotide sequence, genome, dna, dna database, dna research, nucleotide, phylogenetics, protein, sequence, protein binding, gene expression, gene, genetics, nucleoid, genomics, protein binding, gold standard, bio.tools, FASEB list |
is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: OMICtools is listed by: re3data.org is listed by: Debian is listed by: bio.tools is related to: INSDC is related to: GenBank is related to: INSDC is related to: European Nucleotide Archive (ENA) is related to: GenBank is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: Worldwide Protein Data Bank (wwPDB) is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: PDBe - Protein Data Bank in Europe is related to: PDBe - Protein Data Bank in Europe is related to: European Nucleotide Archive (ENA) is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: NCBI Assembly Archive Viewer has parent organization: National Institute of Genetics; Shizuoka; Japan is parent organization of: DDBJ Omics Archive is parent organization of: BodyMap-Xs is parent organization of: DDBJ Sequence Read Archive is parent organization of: CIBEX: Center for Information Biology gene EXpression database is parent organization of: Japanese Genotype-phenotype Archive (JGA) |
Japanese Ministry of Education Culture Sports Science and Technology MEXT | PMID:26578571 PMID:25477381 |
Free, Freely available, | OMICS_01644, biotools:ddbj, nif-0000-02740, r3d100010218 | https://bio.tools/ddbj, https://doi.org/10.17616/R3M01R | SCR_002359 | DNA DataBank of Japan (DDBJ), DNA DataBank of Japan, DDBJ, DNA Data Bank of Japan, DDBJ - DNA Data Bank of Japan | 2026-07-28 09:40:24 | 627 | ||||
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ShotGun Resource Report Resource Website 10+ mentions |
ShotGun (RRID:SCR_002529) | software application, data analysis software, sequence analysis software, software resource, data processing software, simulation software | Software for short read simulating in order to facilitate sequencing-based study designs. | sequence based study design, short read stimulation, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
PMID:23357921 | Free, Available for download, Freely available | biotools:abcd, OMICS_00255 | https://bio.tools/abcd | SCR_002529 | ShotGun: a Flexible Short Read Simulator to Facilitate Sequencing-based Study Designs | 2026-07-28 09:40:26 | 32 | ||||||
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Gibbs Motif Sampler Resource Report Resource Website 1+ mentions |
Gibbs Motif Sampler (RRID:SCR_002550) | Gibbs Motif Sampler | service resource, data analysis service, software resource, production service resource, analysis service resource | Software to identify motifs, conserved regions, in DNA or protein sequences. | dna, protein, motif, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:gibbs_motif_sampler, OMICS_00496 | https://bio.tools/gibbs_motif_sampler | SCR_002550 | The Gibbs Motif Sampler | 2026-07-28 09:40:27 | 2 |
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