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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SPOT - Biological prioritization after a SNP association study Resource Report Resource Website 500+ mentions |
SPOT - Biological prioritization after a SNP association study (RRID:SCR_005193) | SPOT | analysis service resource, data analysis service, production service resource, service resource | A web-based tool for using biological databases to prioritize single nucleotide polymorphisms (SNPs) after a genome-wide association study (GWAS). The site allows users to upload a list of SNPs and GWAS P-values and returns a prioritized list of SNPs using the GIN method. Users can specify candidate genes or genomic regions with custom levels of prioritization. The results can be downloaded or viewed in the browser where users can interactively explore the details of each SNP, including graphical representations of the genomic information network (GIN) method. For investigators interested in incorporating biological databases into a post-GWAS SNP selection strategy, the SPOT web tool is an easily implemented and flexible solution. | single nucleotide polymorphism, genome-wide association study, linkage disequilibrium, gene, genomic region, p-value, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Southern California; Los Angeles; USA |
PMID:20529875 | biotools:spot, OMICS_00189 | https://bio.tools/spot | SCR_005193 | 2026-08-07 09:26:09 | 512 | |||||||
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GoMapMan Resource Report Resource Website 10+ mentions |
GoMapMan (RRID:SCR_005060) | GoMapMan | database, data or information resource, 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 | 2026-08-07 09:26:02 | 29 | |||||
|
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 | 2026-08-07 09:26:04 | 1009 | |||||
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ADGO Resource Report Resource Website 1+ mentions |
ADGO (RRID:SCR_006343) | ADGO | analysis service resource, data analysis service, production service resource, service resource | A web-based tool that provides composite interpretations for microarray data comparing two sample groups as well as lists of genes from diverse sources of biological information. It provides multiple gene set analysis methods for microarray inputs as well as enrichment analyses for lists of genes. It screens redundant composite annotations when generating and prioritizing them. It also incorporates union and subtracted sets as well as intersection sets. Users can upload their gene sets (e.g. predicted miRNA targets) to generate and analyze new composite sets. | microarray, gene, annotation, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:21624890 | Acknowledgement requested | OMICS_02229, biotools:adgo | https://bio.tools/adgo | SCR_006343 | 2026-08-07 09:26:19 | 3 | ||||||
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HMM-TM Resource Report Resource Website 1+ mentions |
HMM-TM (RRID:SCR_006186) | HMM-TM | analysis service resource, data analysis service, production service resource, service resource | A web tool using the Hidden Markov Model method for the topology prediction of alpha-helical membrane proteins that incorporates experimentally derived topological information. Hidden Markov Models (HMMs) have been extensively used in computational molecular biology, for modelling protein and nucleic acid sequences. In many applications, such as transmembrane protein topology prediction, the incorporation of limited amount of information regarding the topology, arising from biochemical experiments, has been proved a very useful strategy that increased remarkably the performance of even the top-scoring methods. However, no clear and formal explanation of the algorithms that retains the probabilistic interpretation of the models has been presented so far in the literature. We present here, a simple method that allows incorporation of prior topological information concerning the sequences at hand, while at the same time the HMMs retain their full probabilistic interpretation in terms of conditional probabilities. We present modifications to the standard Forward and Backward algorithms of HMMs and we also show explicitly, how reliable predictions may arise by these modifications, using all the algorithms currently available for decoding HMMs. A similar procedure may be used in the training procedure, aiming at optimizing the labels of the HMM''s classes, especially in cases such as transmembrane proteins where the labels of the membrane-spanning segments are inherently misplaced. We present an application of this approach developing a method to predict the transmembrane regions of alpha-helical membrane proteins, trained on crystallographically solved data. We show that this method compares well against already established algorithms presented in the literature, and it is extremely useful in practical applications. | hidden markov model, topology, prediction, alpha-helical membrane protein, protein, transmembrane, transmembrane alpha-helical protein, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Athens Biophysics and Bioinformatics Laboratory |
PMID:16597327 | Free for academic use | nlx_151731, biotools:hmm-tm | https://bio.tools/hmm-tm | SCR_006186 | HMM-TM: Prediction of Transmembrane Alpha-Helical Proteins | 2026-08-07 09:26:18 | 7 | |||||
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PRED-LIPO Resource Report Resource Website 10+ mentions |
PRED-LIPO (RRID:SCR_006187) | PRED-LIPO | analysis service resource, data analysis service, production service resource, service resource | A web tool using the Hidden Markov Model method for the prediction of lipoprotein signal peptides of Gram-positive bacteria, trained on a set of 67 experimentally verified lipoproteins. The method outperforms LipoP and the methods based on regular expression patterns, in various data sets containing experimentally characterized lipoproteins, secretory proteins, proteins with an N-terminal TM segment and cytoplasmic proteins. The method is also very sensitive and specific in the detection of secretory signal peptides and in terms of overall accuracy outperforms even SignalP, which is the top-scoring method for the prediction of signal peptides. | hidden markov model, lipoprotein signal peptide, gram-positive bacteria, lipoprotein, prediction, peptide, protein, signal peptide, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Athens Biophysics and Bioinformatics Laboratory |
National Scholarships Foundation of Greece | PMID:19367716 | Free | nlx_151732, biotools:pred-lipo | https://bio.tools/pred-lipo | SCR_006187 | PRED-LIPO: Prediction of Lipoprotein and Secretory Signal Peptides in Gram-positive Bacteria with Hidden Markov Models | 2026-08-07 09:26:18 | 17 | ||||
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PRED-SIGNAL Resource Report Resource Website 10+ mentions |
PRED-SIGNAL (RRID:SCR_006181) | PRED-SIGNAL | analysis service resource, data analysis service, production service resource, service resource | A web tool for prediction of signal peptides in archaea. Computational prediction of signal peptides (SPs) and their cleavage sites is of great importance in computational biology; however, currently there is no available method capable of predicting reliably the SPs of archaea, due to the limited amount of experimentally verified proteins with SPs. We performed an extensive literature search in order to identify archaeal proteins having experimentally verified SP and managed to find 69 such proteins, the largest number ever reported. A detailed analysis of these sequences revealed some unique features of the SPs of archaea, such as the unique amino acid composition of the hydrophobic region with a higher than expected occurrence of isoleucine, and a cleavage site resembling more the sequences of gram-positives with almost equal amounts of alanine and valine at the position-3 before the cleavage site and a dominant alanine at position-1, followed in abundance by serine and glycine. Using these proteins as a training set, we trained a hidden Markov model method that predicts the presence of the SPs and their cleavage sites and also discriminates such proteins from cytoplasmic and transmembrane ones. | signal peptide, prediction, protein, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Athens Biophysics and Bioinformatics Laboratory |
State Scholarships Foundation of Greece | PMID:18988691 | Free for academic use | biotools:pred-signal, nlx_151728 | https://bio.tools/pred-signal | SCR_006181 | PRED-SIGNAL - Prediction of Signal Peptides in Archaea with Hidden Markov Models | 2026-08-07 09:26:18 | 14 | ||||
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FuncAssociate: The Gene Set Functionator Resource Report Resource Website 10+ mentions |
FuncAssociate: The Gene Set Functionator (RRID:SCR_005768) | FuncAssociate | analysis service resource, data analysis service, production service resource, service resource | A web-based tool that accepts as input a list of genes, and returns a list of GO attributes that are over- (or under-) represented among the genes in the input list. Only those over- (or under-) representations that are statistically significant, after correcting for multiple hypotheses testing, are reported. Currently 37 organisms are supported. In addition to the input list of genes, users may specify a) whether this list should be regarded as ordered or unordered; b) the universe of genes to be considered by FuncAssociate; c) whether to report over-, or under-represented attributes, or both; and d) the p-value cutoff. A new version of FuncAssociate supports a wider range of naming schemes for input genes, and uses more frequently updated GO associations. However, some features of the original version, such as sorting by LOD or the option to see the gene-attribute table, are not yet implemented. Platform: Online tool | gene, gene ontology, statistical analysis, web service, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology has parent organization: Roth Laboratory |
NIH ; Canadian Institute for Advanced Research ; NINDS NS054052; NINDS NS035611; NHLBI HL081341; NHGRI HG0017115; NHGRI HG004233; NHGRI HG003224 |
PMID:19717575 PMID:14668247 |
Free for academic use, Acknowledgement requested | biotools:funcassociate, OMICS_02264, nlx_149233 | http://llama.mshri.on.ca/cgi/func/funcassociate, https://bio.tools/funcassociate | SCR_005768 | 2026-08-07 09:26:13 | 36 | |||||
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WEGO - Web Gene Ontology Annotation Plot Resource Report Resource Website 100+ mentions |
WEGO - Web Gene Ontology Annotation Plot (RRID:SCR_005827) | WEGO | analysis service resource, data analysis service, production service resource, service resource | Web Gene Ontology Annotation Plot (WEGO) is a simple but useful tool for plotting Gene Ontology (GO) annotation results. Different from other commercial software for chart creating, WEGO is designed to deal with the directed acyclic graph (DAG) structure of GO to facilitate histogram creation of GO annotation results. WEGO has been widely used in many important biological research projects, such as the rice genome project and the silkworm genome project. It has become one of the useful tools for downstream gene annotation analysis, especially when performing comparative genomics tasks. Platform: Online tool | visualization, gene ontology, gene, annotation, comparative genomics, histogram, directed acyclic graph, genomics, genome, ontology or annotation visualization, bio.tools |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: BGI; Shenzhen; China |
Zhejiang University ; Chinese Academy of Sciences ; Danish Basic Research Foundation ; Ministry of Science and Technology 2002AA104250; Ministry of Science and Technology CNGI-04-15-7A; National Natural Science Foundation of China 30399120; National Natural Science Foundation of China 90208019; National Natural Science Foundation of China 30200163; National Natural Science Foundation of China 90403130 |
PMID:16845012 | Free for academic use | biotools:wego, nlx_149334 | https://bio.tools/wego | SCR_005827 | BGI WEGO - Web Gene Ontology Annotation Plotting, Web Gene Ontology Annotation Plot | 2026-08-07 09:26:11 | 398 | ||||
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SNPsandGO Resource Report Resource Website 50+ mentions |
SNPsandGO (RRID:SCR_005788) | SNPs&GO | analysis service resource, data analysis service, production service resource, service resource | A server for the prediction of single point protein mutations likely to be involved in the insurgence of diseases in humans. | prediction, protein, mutation, disease, single nucleotide polymorphism, bio.tools |
is used by: HmtVar is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: University of Bologna; Bologna; Italy |
PMID:19514061 | biotools:snps_go, OMICS_02219 | https://bio.tools/snps_go | SCR_005788 | SNPs and GO | 2026-08-07 09:26:13 | 61 | ||||||
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waviCGH Resource Report Resource Website 1+ mentions |
waviCGH (RRID:SCR_006662) | waviCGH | analysis service resource, data analysis service, production service resource, service resource | A versatile web-server application for the analysis and visualization of array-CGH data. | genomic, copy number alteration, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:20507915 | Acknowledgement requested | OMICS_00739, biotools:wavicgh | https://bio.tools/wavicgh | SCR_006662 | 2026-08-07 09:26:23 | 4 | ||||||
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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 | 2026-08-07 09:26:42 | 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 | BhairPred | 2026-08-07 09:26:45 | 2 | |||||||
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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 | Genome Function INtegrated Discoverer, Genome Function INtegrated Discoverer (GFINDer) | 2026-08-07 09:26:49 | 1 | |||||
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CRCView Resource Report Resource Website |
CRCView (RRID:SCR_007092) | CRCView | analysis service resource, data analysis service, production service resource, service resource | Web-based microarray data analysis and visualization system powered by CRC, or Chinese Restaurant cluster, a Dirichlet process model-based clustering algorithm recently developed by Dr. Steve Qin. It also incorporates several gene expression analysis programs from Bioconductor, including GOStats, genefilter, and Heatplus. CRCView also installs from the Bioconductor system 78 annotation libraries of microarray chips for human (31), mouse (24), rat (14), zebrafish (1), chicken (1), Drosophila (3), Arabidopsis (2), Caenorhabditis elegans (1), and Xenopus Laevis (1). CRCView allows flexible input data format, automated model-based CRC clustering analysis, rich graphical illustration, and integrated Gene Ontology (GO)-based gene enrichment for efficient annotation and interpretation of clustering results. CRC has the following features comparing to other clustering tools: 1) able to infer number of clusters, 2) able to cluster genes displaying time-shifted and/or inverted correlations, 3) able to tolerate missing genotype data and 4) provide confidence measure for clusters generated. You need to register for an account in the system to store your data and analyses. The data and results can be visited again anytime you log in. | microarray, gene expression, cluster, gene, expression profile, data repository, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Bioconductor is related to: Gene Ontology has parent organization: University of Michigan; Ann Arbor; USA |
University of Michigan; Michigan; USA ; Institutional Fund ; NIH U013422; NIAID 1R21AI057875-01 |
PMID:17485426 | Registration required | biotools:crcview, nlx_99864 | https://bio.tools/crcview | http://helab.bioinformatics.med.umich.edu/crcview/ | SCR_007092 | Chinese Restaurant ClusterView | 2026-08-07 09:26:29 | 0 | |||
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ESEfinder 3.0 Resource Report Resource Website 100+ mentions |
ESEfinder 3.0 (RRID:SCR_007088) | ESEfinder | analysis service resource, data analysis service, production service resource, service resource | A web-based resource that facilitates rapid analysis of exon sequences to identify putative exonic splicing enhancers (ESEs) responsive to the human SR proteins SF2/ASF, SC35, SRp40 and SRp55, and to predict whether exonic mutations disrupt such elements. | exonic splicing enhancer, sr protein, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Cold Spring Harbor Laboratory |
NIGMS GM42699; NCI CA88351; NHGRI HG01696 |
PMID:12824367 | Free for non-profit use, Non-commercial, Acknowledgement requested, Commercial use with license | biotools:esefinder, nif-0000-30496 | http://rulai.cshl.edu/tools/ESE2/, https://bio.tools/esefinder | http://exon.cshl.edu/ESE/ | SCR_007088 | 2026-08-07 09:26:28 | 213 | ||||
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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 | ExpressYourself: microarray data processing platform, Express Yourself, Express Yourself: microarray data processing platform | 2026-08-07 09:26:50 | 0 | |||||||
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AceDB Resource Report Resource Website 10+ mentions |
AceDB (RRID:SCR_010671) | database, data or information resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 6th,2023. Software genome database management system. | genome database management system, genome database, management system, |
is listed by: Debian is listed by: OMICtools is related to: ESTHER has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
DOI:10.1109/5992.764215 | THIS RESOURCE IS NO LONGER IN SERVICE. | nlx_75315, OMICS_15828 | https://sources.debian.org/src/acedb-other/ | SCR_010671 | A C. elegans DataBase | 2026-08-07 09:27:22 | 12 | ||||||
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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 | Vector Alignment Search Tool (VAST) | 2026-08-07 09:27:19 | 17 | ||||||
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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 | 2026-08-07 09:27:09 | 18 |
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