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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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miROrtho: the catalogue of animal microRNA genes Resource Report Resource Website 1+ mentions |
miROrtho: the catalogue of animal microRNA genes (RRID:SCR_007797) | data or information resource, database | It contains predictions of precursor miRNA genes covering several animal genomes combining orthology and a Support Vector Machine. We provide homology extended alignments of already known miRBase families and putative miRNA families exclusively predicted by our SVM and orthology pipeline. The current release of miROrtho covers 46 animal genomes. We provide homology extended alignments of already known miRBase families and putative miRNA families exclusively predicted by our SVM and orthology pipeline. | bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Geneva; Geneva; Switzerland |
nif-0000-03139, biotools:mirortho | https://bio.tools/mirortho | SCR_007797 | SciCrunch Registry | miROrtho | 2026-09-26 02:18:36 | 4 | ||||||||
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Alternate splicing gallery Resource Report Resource Website 1+ mentions |
Alternate splicing gallery (RRID:SCR_008129) | data or information resource, database | Alternative splicing essentially increases the diversity of the transcriptome and has important implications for physiology, development and the genesis of diseases. This resource uses a different approach to investigate alternative splicing (instead of the conventional case-by case fashion) and integrates all transcripts derived from a gene into a single splicing graph. ASG is a database of splicing graphs for human genes, using transcript information from various major sources (Ensembl, RefSeq, STACK, TIGR and UniGene). Each transcript corresponds to a path in the graph, and alternative splicing is displayed by bifurcations. This representation preserves the relationships between different splicing variants and allows us to investigate systematically all possible putative transcripts. Web interface allows users to display the splicing graphs, to interactively assemble transcripts and to access their sequences as well as neighboring genomic regions. ASG also provide for each gene, an exhaustive pre-computed catalog of putative transcriptsin total more than 1.2 million sequences. It has found that ~65 of the investigated genes show evidence for alternative splicing, and in 5 of the cases, a single gene might produce over 100 transcripts. | gallery, gene, genesis, alternative, development, disease, diversity, genomic, human, physiology, putative transcript, sequence, single, splice, splicing graph, transcript, transcriptome, variant, bio.tools |
is listed by: bio.tools is listed by: Debian |
nif-0000-20932, biotools:alternative_splicing_gallery | https://bio.tools/alternative_splicing_gallery | SCR_008129 | SciCrunch Registry | ASG | 2026-09-26 02:18:40 | 1 | ||||||||
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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 | 2026-09-26 02:18:41 | 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 | 2026-09-26 02:18:41 | 5 | ||||||
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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 | 2026-09-26 02:18:42 | 2 | |||||||
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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 | 2026-09-26 02:18:44 | 4 | |||||
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ArrayPipe Resource Report Resource Website 10+ mentions |
ArrayPipe (RRID:SCR_010934) | ArrayPipe | analysis service resource, data analysis service, production service resource, service resource | A flexible tool for visualizing and analyzing your two-colour microarray slides. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00744, biotools:arraypipe | https://bio.tools/arraypipe | SCR_010934 | SciCrunch Registry | 2026-09-26 02:18:47 | 15 | ||||||||
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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 | 2026-09-26 02:18:44 | 718 | ||||||||
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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) | 2026-09-26 02:18:43 | 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 | 2026-09-26 02:18:44 | 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 | 2026-09-26 02:18:44 | 35 | ||||
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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 | 2026-09-26 02:18:43 | 0 | |||||||
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DIANA-LncBase Resource Report Resource Website 100+ mentions |
DIANA-LncBase (RRID:SCR_010840) | LncBase | data or information resource, database | Database that hosts elaborated information for both predicted and experimentally verified, miRNA-lncRNA interactions. The database consists of two distinct modules. The Experimental Module contains detailed information for more than 5,000 interactions, between 2,958 lncRNAs and 120 miRNAs, ranging from miRNA and lncRNA related facts to information specific to their interaction, the experimental validation methodologies and their outcomes. The Prediction Module, which is based on the latest version of DIANA-microT target prediction algorithm (DIANA-microT-CDS), contains detailed information for more than 10 million interactions, between 56,097 lncRNAs and 3,078 miRNAs, ranging from miRNA and lncRNA related details to specific information regarding their interaction sites, graphical representation of their binding and the predicted score. This module exhibits a unique feature for searching the database. Users are able to add genomic locations to their queries thus browsing every miRNA-lncRNA interaction that has at least one MRE located inside the queried locus. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23193281 | biotools:diana-lncbase, OMICS_00396 | https://bio.tools/diana-lncbase | SCR_010840 | SciCrunch Registry | 2026-09-26 02:18:47 | 169 | |||||||
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RACE Resource Report Resource Website 100+ mentions |
RACE (RRID:SCR_010950) | RACE | analysis service resource, data analysis service, production service resource, service resource | A collection of web tools designed to assist with the analysis of DNA microarray data and results. RACE performs probe level data preprocessing, quality checks, normalization, and visualization for Affymetrix GeneChips. In addition, it performs clustering and differential analysis of normalized expression levels or ratios for arbitrary platforms, and estimates the false discovery rates in lists of potentially regulated genes. A Gene Ontology (GO)-term analysis assists in the biological interpretation of gene lists. The user can customize each analysis request; upon submission the analysis is executed in a fully automated way., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | dna microarray, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Lausanne; Lausanne; Switzerland |
PMID:15980552 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00777, biotools:race | https://bio.tools/race | SCR_010950 | SciCrunch Registry | Remote Analysis Computation for gene Expression data | 2026-09-26 02:18:47 | 357 | |||||
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Pscan-ChIP Resource Report Resource Website 1+ mentions |
Pscan-ChIP (RRID:SCR_010885) | Pscan-ChIP | analysis service resource, data analysis service, production service resource, service resource | Web server that, starting from a collection of genomic regions derived from a ChIP-Seq experiment, scans them using motif descriptors like JASPAR or TRANSFAC position-specific frequency matrices, or descriptors uploaded by users, and it evaluates both motif enrichment and positional bias within the regions according to different measures and criteria. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23748563 DOI:10.1093/nar/gkt448 |
biotools:pscanchip, OMICS_00490 | https://bio.tools/pscanchip, https://sources.debian.org/src/pscan-chip/ | SCR_010885 | SciCrunch Registry | 2026-09-26 02:18:47 | 6 | |||||||
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CUPSAT Resource Report Resource Website 50+ mentions |
CUPSAT (RRID:SCR_010773) | CUPSAT | analysis service resource, data analysis service, production service resource, service resource | A tool to predict changes in protein stability upon point mutations. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:16845001 | biotools:cupsat, OMICS_00128 | https://bio.tools/cupsat | SCR_010773 | SciCrunch Registry | Cologne University Protein Stability Analysis Tool, CUPSAT: Cologne University Protein Stability Analysis Tool | 2026-09-26 02:18:47 | 86 | ||||||
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LS-SNP/PDB Resource Report Resource Website 1+ mentions |
LS-SNP/PDB (RRID:SCR_010774) | LS-SNP/PDB | analysis service resource, data analysis service, production service resource, service resource | A web tool for genome-wide annotation of human SNPs. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Johns Hopkins University; Maryland; USA |
OMICS_00131, biotools:ls-snp | https://bio.tools/ls-snp | SCR_010774 | SciCrunch Registry | 2026-09-26 02:18:47 | 3 | ||||||||
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Vector Alignment Search Tool Resource Report Resource Website 10+ mentions |
Vector Alignment Search Tool (RRID:SCR_010655) | VAST | analysis service resource, production service resource, service resource | VAST is a computer algorithm developed at NCBI and used to identify similar protein 3-dimensional structures by purely geometric criteria, and to identify distant homologs that cannot be recognized by sequence comparison. Related structures for every structure in MMDB are pre-computed using VAST and accessible via links on the MMDB Structure Summary pages. The VAST Search page also allows you to compare the coordinates of a newly resolved structure in PDB format against all structures in MMDB to find its neighbors. Protein structure neighbors in Entrez are determined by direct comparison of 3-dimensional protein structures with the VAST algorithm. Each of the more than 87,804 domains in MMDB is compared to every other one. From the MMDB Structure summary pages, retrieved via Entrez, structure neighbors are available for protein chains and individual structural domains. If you already know a PDB/MMDB-Id you can try this at once, using the input form in the right column. VAST Search is a service that allows searching for structural neighbors starting with a set of 3D-coordinates specified by the user. This service is meant to be used with newly determined protein structures that are not yet part of MMDB. Structure neighbors for proteins already in MMDB have been pre-computed and can simply be looked up from MMDB''s Structure summary pages! | gold standard, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: NCBI Structure has parent organization: NCBI |
PMID:8804824 PMID:8710828 |
nlx_68740, biotools:vast | https://bio.tools/vast | SCR_010655 | SciCrunch Registry | Vector Alignment Search Tool (VAST) | 2026-09-26 02:18:46 | 17 | ||||||
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PlantTFcat Resource Report Resource Website 10+ mentions |
PlantTFcat (RRID:SCR_010898) | PlantTFcat | analysis service resource, data analysis service, production service resource, service resource | A web-based analysis tool that is designed to identify and categorize plant TF/TR/CR genes from genome-scale protein and nucleic acid sequences by systematically analyzing InterProScan domain patterns in protein sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Samuel Roberts Noble Foundation |
PMID:24219505 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:planttfcat, OMICS_00559 | https://bio.tools/planttfcat | SCR_010898 | SciCrunch Registry | PlantTFcat: An Online Plant Transcription Factor and Transcriptional Regulator Categorization and Analysis Tool | 2026-09-26 02:18:47 | 46 | |||||
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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 | 2026-09-26 02:18:44 | 18 |
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