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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Probalign Resource Report Resource Website 10+ mentions |
Probalign (RRID:SCR_013332) | Probalign | software application, data processing software, software resource, alignment software, image analysis software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software that uses partition function posterior probability estimates to compute maximum expected accuracy multiple sequence alignments. Computes maximal expected accuracy multiple sequence alignments from partition function posterior probabilities.Produces accurate alignments on long and heterogeneous length datasets containing protein repeats. |
is used by: eProbalign is listed by: OMICtools is listed by: Debian has parent organization: New Jersey Institute of Technology; New Jersey; USA |
PMID:16954142 DOI:10.1093/bioinformatics/btl472 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00985 | https://sources.debian.org/src/probalign/ | SCR_013332 | Probalign: multiple sequence alignment using partition function posterior probabilities | 2026-02-15 09:20:26 | 16 | ||||||
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GeneSigDB Resource Report Resource Website 10+ mentions |
GeneSigDB (RRID:SCR_013275) | GeneSigDB | data analysis service, software resource, database, data access protocol, web service, service resource, storage service resource, production service resource, data repository, data or information resource, analysis service resource | Database of traceable, standardized, annotated gene signatures which have been manually curated from publications that are indexed in PubMed. The Advanced Gene Search will perform a One-tailed Fisher Exact Test (which is equivalent to Hypergeometric Distribution) to test if your gene list is over-represented in any gene signature in GeneSigDB. Gene expression studies typically result in a list of genes (gene signature) which reflect the many biological pathways that are concurrently active. We have created a Gene Signature Data Base (GeneSigDB) of published gene expression signatures or gene sets which we have manually extracted from published literature. GeneSigDB was creating following a thorough search of PubMed using defined set of cancer gene signature search terms. We would be delighted to accept or update your gene signature. Please fill out the form as best you can. We will contact you when we get it and will be happy to work with you to ensure we accurately report your signature. GeneSigDB is capable of providing its functionality through a Java RESTful web service. | gene, gene signature, curated gene signature, gene expression, gene expression signature, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Dana-Farber Cancer Institute has parent organization: Computational Biology and Functional Genomics Laboratory at Harvard |
Cancer | Genome Research Institute ; Dana-Farber Cancer Institute ; Women's Cancers Program ; Claudia Adams Barr Foundation ; NLM 1R01 LM010129; NCI 1U19 CA148065; NHGRI 1P50 HG004233 |
PMID:22110038 | biotools:genesigdb, nlx_149342 | https://bio.tools/genesigdb | SCR_013275 | Gene Signature Data Base, GeneSigDB - Curated Gene Signatures Database | 2026-02-15 09:20:42 | 24 | ||||
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PlantNATsDB - Plant Natural Antisense Transcripts DataBase Resource Report Resource Website 1+ mentions |
PlantNATsDB - Plant Natural Antisense Transcripts DataBase (RRID:SCR_013278) | PlantNATsDB | data analysis service, database, service resource, production service resource, data or information resource, analysis service resource | Natural Antisense Transcripts (NATs), a kind of regulatory RNAs, occur prevalently in plant genomes and play significant roles in physiological and/or pathological processes. PlantNATsDB (Plant Natural Antisense Transcripts DataBase) is a platform for annotating and discovering NATs by integrating various data sources involving approximately 2 million NAT pairs in 69 plant species. PlantNATsDB also provides an integrative, interactive and information-rich web graphical interface to display multidimensional data, and facilitate plant research community and the discovery of functional NATs. GO annotation and high-throughput small RNA sequencing data currently available were integrated to investigate the biological function of NATs. A ''''Gene Set Analysis'''' module based on GO annotation was designed to dig out the statistical significantly overrepresented GO categories from the specific NAT network. PlantNATsDB is currently the most comprehensive resource of NATs in the plant kingdom, which can serve as a reference database to investigate the regulatory function of NATs. | natural antisense transcript, annotation, high-throughput, small rna sequencing, function, regulatory function, predict, sequence, small rna, blast, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Gene Ontology is related to: Gene Expression Omnibus has parent organization: Zhejiang University; Zhejiang; China |
National Natural Sciences Foundation of China 30971743; National Natural Sciences Foundation of China 31050110121; National Natural Sciences Foundation of China 31071659; Ministry of Science and Technology of China 2009DFA32030; Program for New Century Excellent Talents in University of China NCET-07-0740; Huazhong Agricultural University Scientific and Technological Self-innovation Foundation 2010SC07 |
PMID:22058132 | Free | nlx_151492, biotools:plantnatsdb | https://bio.tools/plantnatsdb | SCR_013278 | Plant Natural Antisense Transcripts DataBase | 2026-02-15 09:20:26 | 9 | ||||
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Dali Server Resource Report Resource Website 500+ mentions |
Dali Server (RRID:SCR_013433) | data analysis service, software resource, service resource, production service resource, analysis service resource | Network service for comparing protein structures in 3D. You submit the coordinates of a query protein structure and Dali compares them against those in the Protein Data Bank (PDB). You receive an email notification when the search has finished. In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences. Requests can also be submitted by e-mail to dali-server at helsinki dot fi. The body of the e-mail message must contain atomic coordinates in PDB format. If you want to know the structural neighbours of a protein already in the Protein Data Bank (PDB), you can find them in the Dali Database. If you want to superimpose two particular structures, you can do it in the pairwise DaliLite server. Academic users may download the DaliLite program for local use. | Protein structure comparison server, protein structure, comparison server, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: University of Helsinki; Helsinki; Finland |
PMID:20457744 | Free, Freely available | biotools:dali | https://bio.tools/dali | SCR_013433 | Dali | 2026-02-15 09:20:46 | 509 | ||||||
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ENIGMA Resource Report Resource Website 100+ mentions |
ENIGMA (RRID:SCR_013400) | software application, data processing software, data analysis software, software resource | A software tool to extract gene expression modules from perturbational microarray data, based on the use of combinatorial statistics and graph-based clustering. The modules are further characterized by incorporating other data types, e.g. GO annotation, protein interactions and transcription factor binding information, and by suggesting regulators that might have an effect on the expression of (some of) the genes in the module. Version : ENIGMA 1.1 used GO annotation version : Aug 29th 2007 | genome, gene, genetic software, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Ghent University; Ghent; Belgium is parent organization of: ENIGMA-DTI Pipeline |
PMID:18402676 | biotools:enigma, nlx_144365 | https://bio.tools/enigma | SCR_013400 | 2026-02-15 09:20:27 | 130 | ||||||||
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EvidenceFinder Resource Report Resource Website 1+ mentions |
EvidenceFinder (RRID:SCR_013764) | web application, software resource | A web application to assist in the identification of articles and research related to literature search terms. The search covers full text articles in the Europe PMC repository. Relevant papers are suggested to users based on the scientific term searched and the selection of questions, generated by the application, relevant to term searched. | web application, software resource, literature search, bio.tools |
is used by: Europe PubMed Central is listed by: Connected Researchers is listed by: Debian is listed by: bio.tools is related to: Connected Researchers is related to: Europe PubMed Central has parent organization: Europe PubMed Central |
Wellcome Trust 098231 | DOI:10.1093/nar/gku1061 | Free, Public | biotools:evidence_finder | https://bio.tools/evidence_finder | SCR_013764 | 2026-02-15 09:20:51 | 3 | ||||||
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Kleborate Resource Report Resource Website 10+ mentions |
Kleborate (RRID:SCR_024051) | software application, data processing software, data analysis software, software resource | Software tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for MLST sequence type, species (e.g. K. pneumoniae, K. quasipneumoniae, K. variicola, etc.), ICEKp associated virulence loci (yersiniabactin (ybt), colibactin (clb), salmochelin (iro), hypermucoidy (rmpA)), virulence plasmid associated loci (salmochelin (iro), aerobactin (iuc), hypermucoidy (rmpA, rmpA2)), antimicrobial resistance determinants (acquired genes, SNPs, gene truncations and intrinsic ?-lactamases), and K (capsule) and O antigen (LPS) serotype prediction, via wzi alleles and Kaptive. | screen genome assemblies, Klebsiella pneumoniae, Klebsiella pneumoniae species complex, genome assemblies, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/kleborate/ | SCR_024051 | KLEBORATE, kleborate | 2026-02-15 09:23:31 | 11 | ||||||||
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IgDiscover Resource Report Resource Website 10+ mentions |
IgDiscover (RRID:SCR_024037) | software application, data processing software, data analysis software, software resource | Software to analyze antibody repertoires and discover new V genes from high-throughput sequencing reads.Heavy chains, kappa and lambda light chains are supported (to discover VH, VK and VL genes)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | analyze antibody repertoires, discover new V genes, high-throughput sequencing reads, | is listed by: Debian | PMID:27995928 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_16456 | https://sources.debian.org/src/igdiscover/ https://github.com/NBISweden/IgDiscover/ |
SCR_024037 | igdiscover | 2026-02-15 09:23:21 | 10 | ||||||
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BOLT-LMM Resource Report Resource Website 1+ mentions |
BOLT-LMM (RRID:SCR_023978) | software application, data processing software, data analysis software, software resource | Software statistical tool for identifying genetic associations. Used for genome wide association studies in large cohorts. | statistical tool, identifying genetic associations, genome wide association studies, large cohorts, | is listed by: Debian | PMID:25642633 | Free, Available for download, Freely available | OMICS_13504 | https://sources.debian.org/src/bolt-lmm/ | SCR_023978 | bolt-lmm | 2026-02-15 09:22:34 | 2 | ||||||
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IVA Resource Report Resource Website 1+ mentions |
IVA (RRID:SCR_024044) | software application, data processing software, data analysis software, software resource | Software tool as de novo assembler designed to assemble virus genomes that have no repeat sequences,using Illumina read pairs sequenced from mixed populations at extremely high and variable depth. | de novo assembler, assemble virus genomes, no repeat sequences, Illumina reads, pairs sequenced from mixed populations, | is listed by: Debian | PMID:25725497 | Free, Available for download, Freely available, | OMICS_08188 | https://sources.debian.org/src/iva/ http://sanger-pathogens.github.io/iva/ |
SCR_024044 | Iterative Virus Assembler - de novo virus assembler of Illumina paired reads., iva | 2026-02-15 09:22:35 | 1 | ||||||
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CONTRAfold Resource Report Resource Website 1+ mentions |
CONTRAfold (RRID:SCR_023994) | CONTRAfold | software application, simulation software, software resource | Software novel secondary structure prediction method based on conditional log-linear models, a flexible class of probabilistic models which generalize upon SCFGs by using discriminative training and feature-rich scoring. Used for sequence prediction. | sequence prediction, | is listed by: Debian | PMID:16873527 | Free, Available for download, Freely available | OMICS_03452 | https://sources.debian.org/src/CONTRAfold/ | SCR_023994 | CONditional TRAining for RNA Secondary Structure Prediction, contrafold | 2026-02-15 09:22:34 | 2 | |||||
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CodonW Resource Report Resource Website 100+ mentions |
CodonW (RRID:SCR_023989) | software application, data processing software, data analysis software, software resource | Software tool designed to simplify Multivariate analysis (correspondence analysis) of codon and amino acid usage. It also calculates standard indices of codon usage. | Multivariate analysis, correspondence analysis, codon and amino acid usage, calculate standard indices, codon usage, | is listed by: Debian | Free, Available for download, Freely available | OMICS_08756 | https://sources.debian.org/src/codonw/ | SCR_023989 | codonw | 2026-02-15 09:23:20 | 193 | |||||||
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EMPeror Resource Report Resource Website 1+ mentions |
EMPeror (RRID:SCR_024013) | web application, software resource | Web browser enabled tool with versatile command line interface to perform exploratory investigations of 3D visualizations of microbial community data, such as principal coordinates plots. EMPeror includes set of controllers to modify features as function of metadata. Web interactive next generation tool for analysis, visualization and understanding of high throughput microbial ecology datasets. | visualizing high-throughput microbial community data, | is listed by: Debian | PMID:24280061 | Free, Available for download, Freely available | https://sources.debian.org/src/emperor/ | SCR_024013 | EMPEROR, Emperor, emperor | 2026-02-15 09:23:20 | 6 | |||||||
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EMBOSS explorer Resource Report Resource Website 1+ mentions |
EMBOSS explorer (RRID:SCR_024014) | web application, software resource | Web based graphical user interface to the EMBOSS suite of bioinformatics tools. | graphical user interface, EMBOSS suite, bioinformatics tools, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/emboss-explorer/ | SCR_024014 | emboss-explorer | 2026-02-15 09:23:17 | 1 | ||||||||
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Filtlong Resource Report Resource Website 100+ mentions |
Filtlong (RRID:SCR_024020) | software application, data processing software, software resource | Software tool for filtering long reads by quality.Can take set of long reads and produce smaller, better subset. Uses both read length and read identity when choosing which reads pass the filter. | filtering long reads by quality, read length, read identity, filtering reads, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/filtlong/ | SCR_024020 | filtlong | 2026-02-15 09:23:17 | 309 | ||||||||
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CTSim Resource Report Resource Website |
CTSim (RRID:SCR_024004) | software application, simulation software, software resource | Software tool to simulate process of transmitting X-rays through phantom objects. Reconstructs original phantom image from projections. Has wide array of image analysis and image processing functions. | Computed tomography simulator, reconstruct original phantom image from projections, reconstruct image, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/ctsim/ | SCR_024004 | ctsim, Open Source Computed Tomography Simulator | 2026-02-15 09:23:17 | 0 | ||||||||
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IGoR Resource Report Resource Website 10+ mentions |
IGoR (RRID:SCR_024053) | software application, data processing software, data analysis software, software resource | C++ software designed to infer V(D)J recombination related processes from sequencing data. | infer V(D)J recombination related processes, sequencing data, | is listed by: Debian | PMID:29422654 | Free, Available for download, Freely available, | OMICS_18534 | https://sources.debian.org/src/igor/ https://qmarcou.github.io/IGoR/ |
SCR_024053 | Inference and Generation Of Repertoires, igor | 2026-02-15 09:23:21 | 13 | ||||||
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Proteinortho Resource Report Resource Website 50+ mentions |
Proteinortho (RRID:SCR_024177) | software application, data processing software, data analysis software, software resource | Software tool to detect orthologous genes within different species. Stand-alone tool for large datasets for orthology analysis. | Stand-alone tool, detect orthologous genes, different species, large datasets, orthology analysis, | is listed by: Debian | PMID:21526987 | Free, Available for download, Freely available, | OMICS_05355 | https://sources.debian.org/src/proteinortho/ | SCR_024177 | 2026-02-15 09:22:37 | 97 | |||||||
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KmerResistance Resource Report Resource Website |
KmerResistance (RRID:SCR_024058) | software application, data processing software, data analysis software, software resource | Software tool to correlate mapped genes with the predicted species of WGS samples, where this allows for identification of genes in samples which have been poorly sequenced or high accuracy predictions for samples with contamination. KmerResistance has one dependency, namely KMA to perform the mapping, which is also freely available. | correlate mapped genes, predicted species, WGS samples, identification of genes, | is listed by: Debian | PMID:27365186 | Free, Available for download, Freely available, | https://sources.debian.org/src/kmerresistance/ | SCR_024058 | kmerresistance | 2026-02-15 09:23:18 | 0 | |||||||
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PROFisis Resource Report Resource Website |
PROFisis (RRID:SCR_024179) | software application, simulation software, software resource | Software tool that identifies interacting residues from sequence alone. Developed using transient protein�protein interfaces from complexes of experimentally known 3D structures. | identifies interacting residues from sequence alone, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_13706 | https://sources.debian.org/src/profisis/ | SCR_024179 | profisis | 2026-02-15 09:23:22 | 0 |
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