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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MG-RAST Resource Report Resource Website 1000+ mentions |
MG-RAST (RRID:SCR_004814) | MG RAST | analysis service resource, data analysis service, production service resource, service resource | An automated analysis platform for metagenomes providing quantitative insights into microbial populations based on sequence data. The server primarily provides upload, quality control, automated annotation and analysis for prokaryotic metagenomic shotgun samples. | metagenome, base pair, sequence, phylogenetic, functional analysis, data sharing, metadata, protein, micro biome, analysis platform, bio.tools |
is listed by: OMICtools is listed by: Human Microbiome Project is listed by: Debian is listed by: bio.tools has parent organization: Argonne National Laboratory |
NIAID contract HHSN272200900040C; DOE contract DE-AC02-06CH11357 |
PMID:18803844 | Acknowledgement requested, Public, Account required | OMICS_01456, biotools:mg-rast | http://metagenomics.nmpdr.org, https://bio.tools/mg-rast | SCR_004814 | SciCrunch Registry | The Metagenomics RAST server, Metagenomics RAST, MG-RAST - metagenomics analysis server | 2026-10-24 12:50:31 | 1165 | ||||
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GoMapMan Resource Report Resource Website 10+ mentions |
GoMapMan (RRID:SCR_005060) | GoMapMan | data or information resource, database, service resource | An open web-accessible resource for gene functional annotations in the plant sciences to facilitate improvement, consolidation and visualization of gene annotations across several plant species. It is based on the MapMan ontology, organized in the form of a hierarchical tree of biological concepts, which describe gene functions. Currently, genes of the model species Arabidopsis, potato, tomato, rice, and tobacco are included. The main features are (i) dynamic and interactive gene product annotation through various curation options; (ii) consolidation of gene annotations for different plant species through the integration of orthologue group information; (iii) traceability of gene ontology changes and annotations; (iv) integration of external knowledge about genes from different public resources; and (v) providing gathered information to high-throughput analysis tools via dynamically generated export files. All of the GoMapMan functionalities are openly available, with the restriction on the curation functions, which require prior registration to ensure traceability of the implemented changes. | functional annotation, function, annotation, gene, visualization, ortholog, ontology, microarray, gene annotation, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Set Enrichment Analysis is related to: MapMan is related to: Biomine is related to: SEGS has parent organization: Jozef Stefan Institute; Ljubljana; Slovenia |
Slovenian Research Agency J4-2228; Slovenian Research Agency P2-0103 |
PMID:24194592 | Creative Commons Attribution-NonCommercial-ShareAlike License | biotools:gomapman, OMICS_02280 | https://bio.tools/gomapman | SCR_005060 | SciCrunch Registry | 2026-10-24 12:50:32 | 29 | |||||
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Human Splicing Finder Resource Report Resource Website 1000+ mentions |
Human Splicing Finder (RRID:SCR_005181) | HSF | analysis service resource, data analysis service, production service resource, service resource | Software tool to help study pre-mRNA splicing and to better understand intronic and exonic mutations leading to splicing defects. To calculate the consensus values of potential splice sites and search for branch points, new algorithms were developed. Furthermore, they have integrated all available matrices to identify exonic and intronic motifs, as well as new matrices to identify hnRNP A1, Tra2-? and 9G8. | splicing, mutation, splicing signal, sequence, transcript, nucleotide, exon, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Ensembl has parent organization: National Institute of Health and Medical Research; Rennes; France |
PMID:19339519 | Acknowledgement requested | biotools:human_splicing_finder, OMICS_00176 | https://bio.tools/human_splicing_finder | http://www.umd.be/HSF/ | SCR_005181 | SciCrunch Registry | 2026-10-24 12:50:33 | 1009 | |||||
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Apo and Holo structures DataBase Resource Report Resource Website 1+ mentions |
Apo and Holo structures DataBase (RRID:SCR_004800) | AH-DB | data or information resource, database | Database of apo and holo structure pairs of proteins before and after binding. Various protein functions have been shown directly associated with conformational transitions triggered by binding other molecules. Tertiary structures determined in the unbound and bound state are usually named apo and holo structures, respectively. AH-DB is the largest database of apo-holo structure pairs and provides a sophisticated interface to search and view the collected data. It contains 746314 apo-holo pairs of 3638 proteins from 702 organisms. | ah-db, ahdb, apo, holo, protein interaction, structural change, protein, protein structure, protein binding, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: National Cheng Kung University; Tainan; Taiwan |
National Science Council Taiwan NSC 99-2628-E-006-017 | PMID:22084200 | The community can contribute to this resource | biotools:ah-db, nlx_143908 | https://bio.tools/ah-db | SCR_004800 | SciCrunch Registry | Apo-Holo DataBase | 2026-10-24 12:50:31 | 1 | ||||
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NCBI BioProject Resource Report Resource Website 10000+ mentions |
NCBI BioProject (RRID:SCR_004801) | data or information resource, database | Database of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project. It is a searchable collection of complete and incomplete (in-progress) large-scale sequencing, assembly, annotation, and mapping projects for cellular organisms. Submissions are supported by a web-based Submission Portal. The database facilitates organization and classification of project data submitted to NCBI, EBI and DDBJ databases that captures descriptive information about research projects that result in high volume submissions to archival databases, ties together related data across multiple archives and serves as a central portal by which to inform users of data availability. BioProject records link to corresponding data stored in archival repositories. The BioProject resource is a redesigned, expanded, replacement of the NCBI Genome Project resource. The redesign adds tracking of several data elements including more precise information about a project''''s scope, material, and objectives. Genome Project identifiers are retained in the BioProject as the ID value for a record, and an Accession number has been added. Database content is exchanged with other members of the International Nucleotide Sequence Database Collaboration (INSDC). BioProject is accessible via FTP. | genome sequencing, sequencing, genotype, phenotype, sequence variant, epigenetic, data set, genome, assembly, annotation, mapping, cellular organism, gene mapping, gene expression, biological tag, gene rearrangement, genetic algorithm, genetic code, genetic genealogy, gold standard, bio.tools |
is listed by: 3DVC is listed by: re3data.org is listed by: Debian is listed by: bio.tools is related to: INSDC has parent organization: NCBI |
NLM | PMID:22139929 | Free, Freely available | r3d100013330, nlx_143909, biotools:bioproject | http://www.ncbi.nlm.nih.gov/genomeprj, https://bio.tools/bioproject, https://doi.org/10.17616/R31NJMS2 | http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=genomeprj | SCR_004801 | SciCrunch Registry | NCBI BioProject Database, BioProject | 2026-10-24 12:50:31 | 14025 | ||||
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StSNP Resource Report Resource Website 1+ mentions |
StSNP (RRID:SCR_005417) | StSNP | analysis service resource, data analysis service, production service resource, service resource | A web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00138, biotools:stsnp | https://bio.tools/stsnp | SCR_005417 | SciCrunch Registry | Structure SNP | 2026-10-24 12:50:34 | 3 | |||||||
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PRINSEQ Resource Report Resource Website 1000+ mentions |
PRINSEQ (RRID:SCR_005454) | PRINSEQ | analysis service resource, data analysis service, production service resource, service resource | A publicly available tool that is able to filter, reformat and trim your genomic and metagenomic sequence data and provide you summary statistics for your sequence data. The interactive web interface facilitates visualizations of the results and export functionality for subsequent data processing. The standalone lite version is written in Perl and does not require any non-core Perl modules. The lite version is primarily designed for data preprocessing and does not generate summary statistics in graphical form., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | microbiome, data analysis, genomic sequence data, metagenomic sequence data, summary, perl, bio.tools |
is listed by: OMICtools is listed by: Human Microbiome Project is listed by: Debian is listed by: bio.tools has parent organization: San Diego State University; California; USA |
PMID:21278185 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01068, biotools:prinseq | http://prinseq.sourceforge.net, https://bio.tools/prinseq | SCR_005454 | SciCrunch Registry | PReprocessing and INformation of SEQuences, preprocessing and information of sequences | 2026-10-24 12:50:34 | 1199 | |||||
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TMA Navigator Resource Report Resource Website 1+ mentions |
TMA Navigator (RRID:SCR_005599) | TMA Navigator | analysis service resource, data analysis service, production service resource, service resource | A free web-based service open to all users for analysis of tissue microarray (TMA) data and related information, accommodating categorical, semi-continuous and continuous expression scores. There is no login requirement. | tissue microarray, network, analysis, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23761446 | Acknowledgement requested, Free | biotools:tma_navigator, OMICS_00821 | https://bio.tools/tma_navigator | SCR_005599 | SciCrunch Registry | 2026-10-24 12:50:35 | 5 | ||||||
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MethylomeDB Resource Report Resource Website 1+ mentions |
MethylomeDB (RRID:SCR_005583) | MethylomeDB | data or information resource, database | A database containing genome-wide brain DNA methylation profiles for human and mouse brains. The DNA methylation profiles were generated by Methylation Mapping Analysis by Paired-end Sequencing (Methyl-MAPS) method and analyzed by Methyl-Analyzer software package. The methylation profiles cover over 80% CpG dinucleotides in human and mouse brains in single-CpG resolution. The integrated genome browser (modified from UCSC Genome Browser allows users to browse DNA methylation profiles in specific genomic loci, to search specific methylation patterns, and to compare methylation patterns between individual samples. Two species were included in the Brain Methylome Database: human and mouse. Human postmortem brain samples were obtained from three distinct cortical regions, i.e., dorsal lateral prefrontal cortex (dlPFC), ventral prefrontal cortex (vPFC), and auditory cortex (AC). Human samples were selected from our postmortem brain collection with extensive neuropathological and psychopathological data, as well as brain toxicology reports. The Department of Psychiatry of Columbia University and the New York State Psychiatric Institute have assembled this brain collection, where a validated psychological autopsy method is used to generate Axis I and II DSM IV diagnoses and data are obtained on developmental history, history of psychiatric illness and treatment, and family history for each subject. The mouse sample (strain 129S6/SvEv) DNA was collected from the entire left cerebral hemisphere. The three human brain regions were selected because they have been implicated in the neuropathology of depression and schizophrenia. Within each cortical region, both disease and non-psychiatric samples have been profiled (matching subjects by age and sex in each group). Such careful matching of subjects allows one to perform a wide range of queries with the ability to characterize methylation features in non-psychiatric controls, as well as detect differentially methylated domains or features between disease and non-psychiatric samples. A total of 14 non-psychiatric, 9 schizophrenic, and 6 depression methylation profiles are included in the database. | brain, dna methylation, dorsal lateral prefrontal cortex, ventral prefrontal cortex, auditory cortex, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Columbia University; New York; USA |
NIH ; NHGRI HG002915; NIMH MH074118 |
PMID:22140101 | OMICS_01843, biotools:methylomedb, nlx_146210 | https://bio.tools/methylomedb | SCR_005583 | SciCrunch Registry | MethylomeDB - the Brain Methylome Database, Brain Methylome Database | 2026-10-24 12:50:35 | 1 | |||||
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Gene Array Analyzer Resource Report Resource Website 1+ mentions |
Gene Array Analyzer (RRID:SCR_008323) | GAA | analysis service resource, data analysis service, production service resource, service resource | Data analysis service that allows to process CEL files from Affymetrix, Inc. GeneChip Gene 1.0 ST Arrays to identify alternative splicing. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:22123740 | Acknowledgement requested | OMICS_00759, biotools:gene_array_analyzer | https://bio.tools/gene_array_analyzer | SCR_008323 | SciCrunch Registry | 2026-10-24 12:50:54 | 5 | ||||||
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PDB Finder Resource Report Resource Website 1+ mentions |
PDB Finder (RRID:SCR_008284) | PDB Finder | data or information resource, database | It is a very information rich protein structure database. Unfortunately, the PDB people are not very good at making their data available for search engines. There are several reasons why search engines often fail on the PDB: * The PDB has zillions of small administrative errors * The PDB-format is search-engine unfriendly * Many PDB files are incomplete The PDBFINDER project is a possible solution to these problems. The PDBFINDER holds for each PDB file a structured, search-engine-friendly-formatted entry that holds the data-items most likely needed for people search for certain types of PDB entries. The PDBFINDER is not useful to search in atomic coordinates; it is meant to ad searches in the administrative records of PDB files. Originally, the PDBFINDER was just for searching in PDB files. However, as all the time more people are using the PDBFINDER to aid modelling and database projects, they decided to also produce the so-called PDBFINDER2. The PDBFINDER2 also holds a lot of quality information about the PDB entries. Please only use the PDBFINDER2 if you really need that quality determination aspect because the PDBFINDER2 is five times bigger than the original PDBFINDER. | bio.tools |
is listed by: bio.tools is listed by: Debian |
biotools:pdbfinder, nif-0000-23902 | https://bio.tools/pdbfinder | SCR_008284 | SciCrunch Registry | 2026-10-24 12:50:54 | 1 | ||||||||
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SVM based method for predicting beta hairpin structures in proteins Resource Report Resource Website 1+ mentions |
SVM based method for predicting beta hairpin structures in proteins (RRID:SCR_008349) | analysis service resource, data analysis service, production service resource, service resource | Bhairpred server is based on machine learning technique SVM using single sequence information, evolutionary profile, predicted and observed secondary structure (as obtained using Psipred and DSSP), predicted and observed accessibility values (as obtainned from Netasa and DSSP). The methods were trained and tested on dataset of 2880 proteins and their performance was evaluated on dataset of 534 proteins used by Thornton (PNAS, 2002). Best prediction results were obtained with hybrid approach that combined prediction results from evolutionary profile, predicted secondary structure and accessibility. | evolutionary, information, protein, protein structure prediction, secondary, sequence, single, svm, technique, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Institute of Microbial Technology; Chandigarh; India |
Institute of Microbial Technology | nif-0000-25213, biotools:bhairpred | https://bio.tools/bhairpred | SCR_008349 | SciCrunch Registry | BhairPred | 2026-10-24 12:50:54 | 2 | |||||||
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ExpressYourself Resource Report Resource Website |
ExpressYourself (RRID:SCR_008881) | ExpressYourself | analysis service resource, data analysis service, production service resource, service resource | A fully integrated platform for processing microarray data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00755, biotools:expressyourself | https://bio.tools/expressyourself | SCR_008881 | SciCrunch Registry | ExpressYourself: microarray data processing platform, Express Yourself, Express Yourself: microarray data processing platform | 2026-10-24 12:50:57 | 0 | |||||||
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miRNEST Resource Report Resource Website 1+ mentions |
miRNEST (RRID:SCR_008907) | miRNEST | data or information resource, database | A database of animal, plant and virus microRNA data maintained at the University of Poznan. The database provides: * 9980 miRNA candiates from 420 animal and plant species predicted in Expressed Sequence Tags * predicted targets for plant candidates * RNA-seq reads mapped to candidates from 29 species * external data from 12 databases that includes sequences, polymorphism, expression and regulation. miRNEST 1.0, it contains miRNA from 563 animals, plants and viruses plant species. | microrna, expressed sequence tag, rna-seq read, sequence, polymorphism, mirna sequence, small rna sequence, single nucleotide polymorphism, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Adam Mickiewicz University in Poznan; Poznan; Poland |
European Social Fund ; Adam Mickiewicz University PBWB-08/2011; Polish Ministry of Science and Higher Education N N301 160935; Polish Ministry of Science and Higher Education N N516 441938 |
PMID:22135287 | nlx_151465, biotools:mirnest | http://mirnest.amu.edu.pl, https://bio.tools/mirnest | SCR_008907 | SciCrunch Registry | miRNEST - a database of animal and plant microRNAs | 2026-10-24 12:50:59 | 4 | |||||
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MicroSNiPer Resource Report Resource Website 10+ mentions |
MicroSNiPer (RRID:SCR_009880) | MicroSNiPer | analysis service resource, data analysis service, production service resource, service resource | A web-based application which predicts the impact of a SNP on putative microRNA targets. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: National Institute of Mental Health |
PMID:20809528 | biotools:microsniper, OMICS_00388 | https://bio.tools/microsniper | SCR_009880 | SciCrunch Registry | 2026-10-24 12:50:59 | 18 | |||||||
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Phylogeny.fr Resource Report Resource Website 500+ mentions |
Phylogeny.fr (RRID:SCR_010266) | data or information resource, database | A free, simple to use web service dedicated to reconstructing and analysing phylogenetic relationships between molecular sequences. Phylogeny.fr runs and connects various bioinformatics programs to reconstruct a robust phylogenetic tree from a set of sequences. | bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian |
PMID:18424797 | nlx_156923, biotools:phylogeny.fr | https://bio.tools/phylogeny.fr | SCR_010266 | SciCrunch Registry | 2026-10-24 12:50:58 | 718 | ||||||||
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hiPathDB - human integrated Pathway DB with facile visualization Resource Report Resource Website 1+ mentions |
hiPathDB - human integrated Pathway DB with facile visualization (RRID:SCR_008900) | hiPathDB | data or information resource, database | hiPathDB is an integrated pathway database that combines the curated human pathway data of NCI-Nature PID, Reactome, BioCarta and KEGG. In total, it includes 1661 pathways consisting of 8976 distinct physical entities. (2010.03.09) hiPathDB provides two different types of integration. The pathway-level integration, conceptually a simple collection of individual pathways, was achieved by devising an elaborate model that takes distinct features of four databases into account and subsequently reformatting all pathways in accordance with our model. The entity-level integration creates a single unified pathway that encompasses all pathways by merging common components. Even though the detailed molecular-level information such as complex formation or post-translational modifications tends to be lost, such integration makes it possible to investigate signaling network over the entire pathways and allows identification of pathway cross-talks. Another strong merit of hiPathDB is the built-in pathway visualization module that supports explorative studies of complex networks in an interactive fashion. The layout algorithm is optimized for virtually automatic visualization of the pathways. | pathway, gene, compound, interaction, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: KEGG is related to: BioCarta Pathways is related to: Reactome is related to: Pathway Interaction Database has parent organization: Korea Research Institute of Bioscience and Biotechnology; Daejeon; South Korea |
Ewha Womans University; Seoul; Korea ; Korean Ministry of Education Science and Technology 2011-000232; Korean Ministry of Education Science and Technology 2011-0019745; Korean Ministry of Education Science and Technology R15-2006-020 |
PMID:22123737 | nlx_151413, biotools:hipathdb | https://bio.tools/hipathdb | SCR_008900 | SciCrunch Registry | Human Integrated Pathway Database | 2026-10-24 12:50:57 | 3 | |||||
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GFINDer: Genome Function INtegrated Discoverer Resource Report Resource Website 1+ mentions |
GFINDer: Genome Function INtegrated Discoverer (RRID:SCR_008868) | GFINDer | analysis service resource, data analysis service, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 16, 2019. Multi-database system providing large-scale lists of user-classified sequence identifiers with genome-scale biological information and functional profiles biologically characterizing the different gene classes in the list. GFINDer automatically retrieves updated annotations of several functional categories from different sources, identifies the categories enriched in each class of a user-classified gene list, and calculates statistical significance values for each category. Moreover, GFINDer enables to functionally classify genes according to mined functional categories and to statistically analyze the obtained classifications, aiding in better interpreting microarray experiment results. | annotation, statistical analysis, mining, genome, function, sequence, functional profile, gene, microarray, bio.tools |
is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology has parent organization: Polytechnic University of Milan; Milan; Italy |
PMID:15980570 PMID:15215397 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149256, biotools:gfinder | https://www.hsls.pitt.edu/obrc/index.php?page=URL1098209538, https://bio.tools/gfinder | SCR_008868 | SciCrunch Registry | Genome Function INtegrated Discoverer, Genome Function INtegrated Discoverer (GFINDer) | 2026-10-24 12:50:57 | 1 | |||||
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mirTools Resource Report Resource Website 10+ mentions |
mirTools (RRID:SCR_009701) | mirTools | analysis service resource, data analysis service, production service resource, service resource | A comprehensive web server developed to allow researchers to comprehensively characterize small RNA transcriptome. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:23778453 | OMICS_00365, biotools:mirtools | https://bio.tools/mirtools | SCR_009701 | SciCrunch Registry | mirTools 2.0 | 2026-10-24 12:50:58 | 13 | ||||||
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Hippocampome.org Resource Report Resource Website 10+ mentions |
Hippocampome.org (RRID:SCR_009023) | Hippocampome | data or information resource, database | A curated knowledge base of the circuitry of the hippocampus of normal adult, or adolescent, rodents at the mesoscopic level of neuronal types. Knowledge concerning dentate gyrus, CA3, CA2, CA1, subiculum, and entorhinal cortex is distilled from published evidence and is continuously updated as new information becomes available. Each reported neuronal property is documented with a pointer to, and excerpt from, relevant published evidence, such as citation quotes or illustrations. Please note: This is an alpha-testing site. The content is still being vetted for accuracy and has not yet undergone peer-review. As such, it may contain inaccuracies and should not (yet) be trusted as a scholarly resource. The content does not yet appear uniformly across all combinations of browsers and screen resolutions. | interneuron, classification, neuroinformatics, network, hippocampus, neuron, property, morphology, molecular marker, electrophysiology, adult, adolescent, dentate gyrus, ca3, ca2, ca1, subiculum, entorhinal cortex, bio.tools |
is used by: BICCN is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools has parent organization: George Mason University; Virginia; USA |
Normal | Air Force Office of Scientific Research ; Office of Naval Research MURI N00014-10-1-0198; NINDS R01NS39600; NINDS R21NS58816 |
Except otherwise noted, Creative Commons Attribution-ShareAlike License | nlx_152892, biotools:Hippocampome.org | http://www.nitrc.org/projects/hippocampome, https://bio.tools/Hippocampome.org | SCR_009023 | SciCrunch Registry | Hippocampome Portal | 2026-10-24 12:50:57 | 35 |
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