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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Kismeth Resource Report Resource Website 50+ mentions |
Kismeth (RRID:SCR_005444) | Kismeth | analysis service resource, data analysis service, production service resource, service resource | A web-based tool for bisulfite sequencing analysis that was designed to be used with plants, since it considers potential cytosine methylation in any sequence context (CG, CHG, and CHH). It provides a tool for the design of bisulfite primers as well as several tools for the analysis of the bisulfite sequencing results. Kismeth is not limited to data from plants, as it can be used with data from any species. | plant, methylation, bisulfite sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
PMID:18786255 | Free for academic use, Contact for commercial use | biotools:kismeth, OMICS_00602 | https://bio.tools/kismeth | SCR_005444 | 2026-09-19 12:56:51 | 55 | ||||||
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TRANSFAC Resource Report Resource Website 100+ mentions |
TRANSFAC (RRID:SCR_005620) | TRANSFAC | data or information resource, database | Manually curated database of eukaryotic transcription factors, their genomic binding sites and DNA binding profiles. Used to predict potential transcription factor binding sites. | Curated, eucaryotic, transcription, factor, genomic, binding, site, sequence, regulated, gene, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: Gene Regulation Databases is related to: TRANSPATH is related to: Babelomics is related to: GeneTrail works with: rVista |
European Commission ; German Ministry of Education and Research |
PMID:12520026 | Free, Freely available | biotools:transfac, nif-0000-03576 | http://www.biobase-international.com/pages/index.php?id=transfac, http://gene-regulation.com/pub/databases.html, https://bio.tools/transfac | SCR_005620 | 2026-09-19 12:56:52 | 266 | |||||
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IndelFR - Indel Flanking Region Database Resource Report Resource Website 1+ mentions |
IndelFR - Indel Flanking Region Database (RRID:SCR_006050) | IndelFR | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Indel Flanking Region Database is an online resource for indels and the flanking regions of proteins in SCOP superfamilies, including amino acid sequences, lengths, locations, secondary structure constitutions, hydrophilicity / hydrophobicity, domain information, 3D structures and so on. It aims at providing a comprehensive dataset for analyzing the qualities of amino acid insertion/deletions(indels), substitutions and the relationship between them. The indels were obtained through the pairwise alignment of homologous structures in SCOP superfamilies. The IndelFR database contains 2,925,017 indels with flanking regions extracted from 373,402 structural alignment pairs of 12,573 non-redundant domains from 1053 superfamilies. IndelFR has already been used for molecular evolution studies and may help to promote future functional studies of indels and their flanking regions. | indel, flanking region, protein, structural domain, domain, protein superfamily, protein structure, insertion/deletion, insertion, deletion, protein sequence, sequence, structure, protein domain, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: SCOP: Structural Classification of Proteins is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: Shandong University; Shandong; China |
Independent Innovation Foundation of Shandong University 2009JC006; National Natural Science Foundation of China 30970092; National Natural Science Foundation of China 61070017; Scientific Research Reward Fund for excellent Young and Middle-Aged scientists in Shandong Province 20090451326 |
PMID:22127860 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:indelfr, nlx_151448 | https://bio.tools/indelfr | SCR_006050 | IndelFR: Indel Flanking Region Database, Indel Flanking Region Database | 2026-09-19 12:56:55 | 2 | ||||
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ProfCom - Profiling of complex functionality Resource Report Resource Website 1+ mentions |
ProfCom - Profiling of complex functionality (RRID:SCR_005797) | ProfCom | analysis service resource, data analysis service, production service resource, service resource | Profiling of Complex Functionality (ProfCom) is a web-based tool for the functional interpretation of a gene list that was identified to be related by experiments. A trait which makes ProfCom a unique tool is an ability to profile enrichments of not only available Gene Ontology (GO) terms but also of complex function. A complex function is constructed as Boolean combination of available GO terms. The complex functions inferred by ProfCom are more specific in comparison to single terms and describe more accurately the functional role of genes. Platform: Online tool | gene, function, profile, gene ontology, complex function, statistical analysis, 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: Institute of Bioinformatics and Systems Biology; Neuherberg; Germany |
DFG | PMID:16959266 | Free for academic use | biotools:profcom, nlx_149276 | https://bio.tools/profcom | SCR_005797 | Profiling of Complex Functionality, Profiling of Complex Functionality (ProfCom) | 2026-09-19 12:56:53 | 4 | ||||
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SerbGO Resource Report Resource Website |
SerbGO (RRID:SCR_005798) | SerbGO | analysis service resource, data analysis service, production service resource, service resource | SerbGO is a web-based tool intended to assist researchers determine which microarray tools for gene expression analysis which make use of the GO ontologies are best suited to their projects. SerbGO is a bidirectional application. The user can ask for some features by checking on the Query Form to get the appropriate tools for their interests. The user can also compare tools to check which features are implemented in each one. Platform: Online tool | microarray, gene expression, statistical analysis, gene ontology, 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: University of Barcelona; Barcelona; Spain |
PMID:18480123 | Free for academic use | nlx_149286, biotools:serbgo | https://bio.tools/serbgo | SCR_005798 | SerbGO - Searching the best GO Tool | 2026-09-19 12:56:54 | 0 | |||||
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SNPedia Resource Report Resource Website 50+ mentions |
SNPedia (RRID:SCR_006125) | SNPedia | data or information resource, database | Wiki investigating human genetics including information about the effects of variations in DNA, citing peer-reviewed scientific publications. It is used by Promethease to analyze and help explain your DNA. It is based on a wiki model in order to foster communication about genetic variation and to allow interested community members to help it evolve to become ever more relevant. As the cost of genotyping (and especially of fully determining your own genomic sequence) continues to drop, we''''ll all want to know more - a lot more - about the meaning of these DNA variations and SNPedia will be here to help. SNPedia has been launched to help realize the potential of the Human Genome Project to connect to our daily lives and well-being. For more information see the Wikipedia page, http://en.wikipedia.org/wiki/SNPedia * Download URL: http://www.SNPedia.com/index.php/Bulk * Web Service URL: http://bots.SNPedia.com/api.php | dna, genetics, gene, genome, genoset, genotype, medicine, medical condition, genetic variation, dna, genetic variation, genomics, single nucleotide polymorphism, medical association, phenotypic association, genealogical association, variation, genome annotation, phenotype, web service, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools |
PMID:22140107 | Creative Commons Attribution-NonCommercial-ShareAlike License, v3 | biotools:snpedia, grid.465250.0, nlx_151604 | https://ror.org/0253rdk33, https://bio.tools/snpedia | SCR_006125 | 2026-09-19 12:56:56 | 64 | ||||||
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RNA CoSSMos Resource Report Resource Website 1+ mentions |
RNA CoSSMos (RRID:SCR_006120) | RNA CoSSMos | data or information resource, database | Database to search through the nucleic acid structures from the Protein Data Bank and examine structural motifs, including (a)symmetric internal loops, bulge loops, and hairpin loops. They have compiled over 2,000 three-dimensional structures, which can now be searched using different parameters, including PDB information, experimental technique, sequence, and motif type. RNA secondary structure is important for designing therapeutics, understanding protein-RNA binding and predicting tertiary structure of RNA. Several databases and downloadable programs exist that specialize in the three-dimensional (3D) structure of RNA, but none focus specifically on secondary structural motifs such as internal, bulge and hairpin loops. To create the RNA CoSSMos database, 2156 Protein Data Bank (PDB) files were searched for internal, bulge and hairpin loops, and each loop''''s structural information, including sugar pucker, glycosidic linkage, hydrogen bonding patterns and stacking interactions, was included in the database. False positives were defined, identified and reclassified or omitted from the database to ensure the most accurate results possible. Users can search via general PDB information, experimental parameters, sequence and specific motif and by specific structural parameters in the subquery page after the initial search. Returned results for each search can be viewed individually or a complete set can be downloaded into a spreadsheet to allow for easy comparison. The RNA CoSSMos database is updated weekly. | secondary structure motif, rna, three-dimensional structure, internal loop, bulge loop, hairpin loop, motif, nucleic acid, structure, secondary structure, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: Saint Louis University; Missouri; USA |
NIGMS 1R15GM085699-01A1 | PMID:22127861 | Freely accessible, Acknowledgement requested | nlx_151597, biotools:rna_cossmos | https://bio.tools/rna_cossmos | SCR_006120 | Znosko Lab RNA Characterization of Secondary Structure Motifs (RNA CoSSMos) database, Znosko Lab CoSSMos Database, RNA Characterization of Secondary Structure Motifs (RNA CoSSMos), RNA CoSSMos Database, RNA CoSSMos - Characterization of Secondary Structure Motifs, RNA Characterization of Secondary Structure Motifs | 2026-09-19 12:56:56 | 1 | ||||
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GoPubMed Resource Report Resource Website 10+ mentions |
GoPubMed (RRID:SCR_005823) | GoPubMed | data or information resource, database, service resource | A web server which allows users to explore PubMed search results with the Gene Ontology, a hierarchically structured vocabulary for molecular biology. GoPubMed submits a user''''s keywords to PubMed, retrieves the abstracts, detects Gene Ontology terms in the abstracts, displays the subset of Gene Ontology relevant to the original query, and allows the user to browse through the ontology displaying associated papers and their GO annotation. Platform: Online tool | other analysis, literature curation and exploration, gene ontology, pubmed, literature, bio.tools |
is listed by: OMICtools is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology is related to: PubMed has parent organization: Biotechnology Center of the TU Dresden |
European Union IST-2004-506779 | PMID:15980585 | Free for academic use | biotools:gopubmed, nlx_149328, OMICS_01183 | https://bio.tools/gopubmed | SCR_005823 | 2026-09-19 12:56:54 | 29 | |||||
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Expression Profiler Resource Report Resource Website 1+ mentions |
Expression Profiler (RRID:SCR_005821) | Expression Profiler | analysis service resource, data analysis service, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. The EP:GO browser is built into EBI's Expression Profiler, a set of tools for clustering, analysis and visualization of gene expression and other genomic data. With it, you can search for GO terms and identify gene associations for a node, with or without associated subnodes, for the organism of your choice. | other analysis, cluster, analysis, visualization, gene expression, genomic, gene ontology, gene association, microarray, protein-protein interaction, gene, 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: European Bioinformatics Institute |
European Union ; Wellcome Trust ; Estonian Science Foundation 5724; Estonian Science Foundation 5722 |
PMID:15215431 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:expression_profiler, nlx_149323 | https://bio.tools/expression_profiler | SCR_005821 | Expression Profiler at the EBI | 2026-09-19 12:56:54 | 6 | ||||
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NRG-CING Resource Report Resource Website 1+ mentions |
NRG-CING (RRID:SCR_006079) | NRG-CING | data or information resource, database | NRG-CING presents a complete validation report for all 9,000+ wwPDB NMR entries including remediated experimental data such as chemical shifts from BMRB and restraints from NRG . These CING reports are compiled from internal analyses and those by CCPN, DSSP, PROCHECK-NMR/Aqua, ShiftX, Talos+, Vasco, Wattos, and WHAT_CHECK. The NRG-CING website is a collection of CING reports that has been pre-calculated for all PDB files solved by NMR. (See website for more information on CING.) In case the underlying experimental data is available, these have been cleaned up and made syntactically and semantically correct and homogeneous. For many macromolecular NMR ensembles from the Protein Data Bank (PDB) the experiment-based restraint lists used in the structure calculation are accessible, while other experimental data, mainly chemical shift values, are often available from the BioMagResBank. Assessment of the quality of the structural result is paramount to their usage and a combined, integrated repository of both input data and structural results greatly facilitates such an analysis. In addition, the accuracy and precision of the coordinates in these macromolecular NMR ensembles can be improved by recalculations using the available experimental data and present-day software with improved protocols and force fields. Such efforts, however, generally fail on over half of all deposited structures due to the syntactic and semantic heterogeneity of the data and the wide variety of formats used for their deposition. We have combined the cleaned-up restraints information from the NMR Restraints Grid (NRG) database with available chemical shifts from the BioMagResBank in the weekly updated NRG-CING database. Eleven programs, in addition to CING itself, have been included in the NRG-CING production pipeline to arrive at validation reports that list for each entry the potential inconsistencies between the coordinates and the available restraint and chemical shift data. The longitudinal validation of this data yielded a set of indicators that can be used to judge the quality of every macromolecular structure solved with NMR. The cleaned up NMR experimental datasets and the validation reports are freely available. | macromolecular structure, nmr, macromolecule, restraint, chemical shift, validation report, validation, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Worldwide Protein Data Bank (wwPDB) is related to: NMR Restraints Grid is related to: Biological Magnetic Resonance Data Bank (BMRB) has parent organization: Radboud University; Nijmegen; The Netherlands |
Netherlands Organization for Scientific Research (NWO) 700.55.443; Netherlands Bioinformatics Centre (NBIC) ; EU FP6 LSHG-CT-2005-018988; EU FP6 LHSG-CT-2004-512092; EU FP7 261572; Brussels Institute for Research and Innovation BB2B 2010-1-12; NLM LM05799 |
PMID:22139937 | Free | nlx_151486, biotools:nrg-cing | https://bio.tools/nrg-cing | SCR_006079 | 2026-09-19 12:56:55 | 1 | |||||
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ProPortal Resource Report Resource Website 1+ mentions |
ProPortal (RRID:SCR_006112) | ProPortal | data or information resource, database | ProPortal is a database containing genomic, metagenomic, transcriptomic and field data for the marine cyanobacterium Prochlorococcus. Our goal is to provide a source of cross-referenced data across multiple scales of biological organization--from the genome to the ecosystem--embracing the full diversity of ecotypic variation within this microbial taxon, its sister group, Synechococcus and phage that infect them. The site currently contains the genomes of 13 Prochlorococcus strains, 11 Synechococcus strains and 28 cyanophage strains that infect one or both groups. Cyanobacterial and cyanophage genes are clustered into orthologous groups that can be accessed by keyword search or through a genome browser. Users can also identify orthologous gene clusters shared by cyanobacterial and cyanophage genomes. Gene expression data for Prochlorococcus ecotypes MED4 and MIT9313 allow users to identify genes that are up or downregulated in response to environmental stressors. In addition, the transcriptome in synchronized cells grown on a 24-h light-dark cycle reveals the choreography of gene expression in cells in a ''natural'' state. Metagenomic sequences from the Global Ocean Survey from Prochlorococcus, Synechococcus and phage genomes are archived so users can examine the differences between populations from diverse habitats. Finally, an example of cyanobacterial population data from the field is included. | genomic, metagenomic, transcriptomic, field data, marine cyanobacterium, genome, ecosystem, ecotypic variation, microbial taxon, phage, genome, gene, orthologous gene cluster, cyanobacteria, cyanophage genome, population dynamics, microarray, metagenome, protein, cyanophage, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
NSF OCE-0425602; NSF EF0424599; DOE DE-FG02-02ER63445; DOE DE-FG02-08ER64516; DOE DE-FG02-07ER64506; Gordon and Betty Moore Foundation award letter 495.01 |
PMID:22102570 | Public | nlx_151586, biotools:proportal | https://bio.tools/proportal | SCR_006112 | Prochlorococcus Portal | 2026-09-19 12:56:56 | 9 | ||||
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UniParc Resource Report Resource Website 50+ mentions |
UniParc (RRID:SCR_005818) | data or information resource, database | Database that contains publicly available protein sequences with stable and unique identifiers (UPI) which are never removed, changed or reassigned. UniParc tracks sequence changes in the source databases and archives the history of all changes. Information other than protein sequence must be retrieved from the UniParc source databases using the database cross-references. | protein sequence, database, public protein sequence, gold standard, upi, unique protein identifier, identifier, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: UniProt DAS is related to: WormBase is related to: FlyBase is related to: Ensembl is related to: RefSeq has parent organization: UniProt |
Public, Entries are available for download | SCR_004769, nif-0000-03610, r3d100011519, biotools:uniparc, nlx_76940 | https://bio.tools/uniparc, https://doi.org/10.17616/R3X33B | SCR_005818 | UniProt Archive | 2026-09-19 12:56:54 | 98 | |||||||
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Dr.VIS - Human Disease-Related Viral Integration Sites Resource Report Resource Website 1+ mentions |
Dr.VIS - Human Disease-Related Viral Integration Sites (RRID:SCR_005965) | Dr.VIS, Dr. VIS | data or information resource, database | Dr.VIS collects and locates human disease-related viral integration sites. So far, about 600 sites covering 5 virus organisms and 11 human diseases are available. Integration sites in Dr.VIS are located against chromosome, cytoband, gene and refseq position as specific as possible. Viral-cellular junction sequences are extracted from papers and nucleotide databases, and linked to corresponding integration sites Graphic views summarizing distribution of viral integration sites are generated according to chromosome maps. Dr.VIS is built with a hope to facilitate research of human diseases and viruses. Dr.VIS provides curated knowledge of integration sites from chromosome region narrow to genomic position, as well as junction sequences if available. Dr.VIS is an open resource for free. | disease, virus, viral integration, viral integration site, integration site, malignant disease, chromosome region, genomic position, viral-host junction sequence, junction sequence, oncogene, chromosome, catalog, graphic interface, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Tongji University; Shanghai; China |
State Key Basic Research Program 973 2011CB910204; National Natural Science Foundation of China ; Major State Basic Research Development Program ; 863 Hi-Tech Program of China ; National Key Technology R&D Program in the 11th Five Year Plan of China ; Major State Basic Research Development Program of China |
PMID:22135288 | Open - Free to browse and download data in Dr.VIS. | nlx_151323, biotools:dr.vis | http://www.scbit.org/dbmi/drvis, https://bio.tools/dr.vis | SCR_005965 | Dr. VIS - Database of Human Disease-related Viral Integration Sites, Database of Human Disease-related Viral Integration Sites | 2026-09-19 12:56:55 | 1 | ||||
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FunTree Resource Report Resource Website 1+ mentions |
FunTree (RRID:SCR_006014) | FunTree | data or information resource, database | FunTree provides a range of data resources to detect the evolution of enzyme function within distant structurally related clusters within domain super families as determined by CATH. To access the resource enter a specific CATH superfamily code or search for a structure / sequence / function (either via a EC code or KEGG ligand / reaction ID, PDB ID or UniProtKB ID). Or browse the resource via superfamily / function / structure / metabolites & reactions via the menu on the left panel. FunTree is a new resource that brings together sequence, structure, phylogenetic, chemical and mechanistic information for structurally defined enzyme superfamilies. Gathering together this range of data into a single resource allows the investigation of how novel enzyme functions have evolved within a structurally defined superfamily as well as providing a means to analyse trends across many superfamilies. This is done not only within the context of an enzyme''''s sequence and structure but also the relationships of their reactions. Developed in tandem with the CATH database, it currently comprises 276 superfamilies covering 1800 (70%) of sequence assigned enzyme reactions. Central to the resource are phylogenetic trees generated from structurally informed multiple sequence alignments using both domain structural alignments supplemented with domain sequences and whole sequence alignments based on commonality of multi-domain architectures. These trees are decorated with functional annotations such as metabolite similarity as well as annotations from manually curated resources such the catalytic site atlas and MACiE for enzyme mechanisms. | enzyme function, enzyme superfamily, enzyme, sequence, structure, phylogenetic, chemical, mechanistic, functional annotation, superfamily, gold standard, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: CATH: Protein Structure Classification is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: KEGG is related to: UniProtKB has parent organization: European Bioinformatics Institute |
European Molecular Biology Laboratory; Heidelberg; Germany ; BBSRC ; Wellcome Trust 081989/Z/07/A; DOE contract DE-AC02-06CH11357 |
PMID:22006843 | Free | biotools:funtree, nlx_151402 | https://bio.tools/funtree | SCR_006014 | 2026-09-19 12:56:55 | 4 | |||||
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DBETH - Database for Bacterial ExoToxins for Humans Resource Report Resource Website 1+ mentions |
DBETH - Database for Bacterial ExoToxins for Humans (RRID:SCR_005908) | DBETH | data or information resource, database | Database of Bacterial ExoToxins for Human is a database of sequences, structures, interaction networks and analytical results for 229 exotoxins, from 26 different human pathogenic bacterial genus. All toxins are classified into 24 different Toxin classes. The aim of DBETH is to provide a comprehensive database for human pathogenic bacterial exotoxins. DBETH also provides a platform to its users to identify potential exotoxin like sequences through Homology based as well as Non-homology based methods. In homology based approach the users can identify potential exotoxin like sequences either running BLASTp against the toxin sequences or by running HMMER against toxin domains identified by DBETH from human pathogenic bacterial exotoxins. In Non-homology based part DBETH uses a machine learning approach to identify potential exotoxins (Toxin Prediction by Support Vector Machine based approach). | sequence, structure, interaction network, human, pathogen, bacterial genus, toxin, bacteria, exotoxin, homology, homolog, structure, sequence, domain, prediction, mechanism, activity, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: CSIR - Indian Institute of Chemical Biology; Kolkata; India |
Council of Scientific and Industrial Research; New Delhi; India | PMID:22102573 | nlx_149481, biotools:dbeth | https://bio.tools/dbeth | SCR_005908 | Database for Bacterial ExoToxins for Humans | 2026-09-19 12:56:54 | 2 | |||||
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VirusMINT Resource Report Resource Website 10+ mentions |
VirusMINT (RRID:SCR_005987) | VirusMINT | data or information resource, database | A virus protein interactions database that collects and annotates all the interactions between human and viral proteins and integrates this information in the human protein interaction network. It uses the PSI-MI standard and is fully integrated with the MINT database. You can search for any viral or human protein by entering either common names or database identifiers or display a complete viral interactome. | protein interaction, virus, protein, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: PSI-MI is related to: VirHostNet: Virus-Host Network is related to: MINT has parent organization: University of Rome Tor Vergata; Rome; Italy |
Papilloma virus, Human immunodeficiency virus, Epstein-Barr virus, Hepatitis B virus, Hepatitis C virus, Herpes virus, Simian virus 40 | PMID:18974184 | nif-0000-03636, OMICS_01909, biotools:virusmint, r3d100010685 | https://bio.tools/virusmint, https://doi.org/10.17616/R3F890 | SCR_005987 | 2026-09-19 12:56:55 | 18 | ||||||
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Homologous Sequences in Ensembl Animal Genomes Resource Report Resource Website 1+ mentions |
Homologous Sequences in Ensembl Animal Genomes (RRID:SCR_008356) | HOMOLENS | data or information resource, database | Database of homologous genes from Ensembl organisms, structured under ACNUC sequence database management system. It allows to select sets of homologous genes among species, and to visualize multiple alignments and phylogenetic trees. It is possible to search for orthologous genes in a wide range of taxons. HOMOLENS is particularly useful for comparative sequence analysis, phylogeny and molecular evolution studies. More generally, HOMOLENS gives an overall view of what is known about a peculiar gene family. Note that HOMOLENS is split into two databases on this server: HOMOLENS contains the protein sequences while HOMOLENSDNA contains the nucleotide sequences. Protein sequences of HOMOLENS have been generated by translating the CDS of HOMOLENSDNA and using associated cross-references to generate the annotations. | ensembl, evolution, gene, alignment, comparative, homologous, molecular, nucleotide, organism, phylogenetic, phylogeny, protein, sequence, specie, structure, taxon, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Claude Bernard University Lyon 1; Lyon; France |
biotools:homolens, nif-0000-25424 | https://bio.tools/homolens | SCR_008356 | 2026-09-19 12:57:17 | 3 | ||||||||
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Regulatory Sequence Analysis Tools Resource Report Resource Website 100+ mentions |
Regulatory Sequence Analysis Tools (RRID:SCR_008560) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Retrieve-ensembl-seq is included in the software suite regulatory sequence analysis tools (RSAT), allowing instant submission of retrieved sequences to further analysis tools. AVAILABILITY: retrieve-ensembl-seq is integrated in the RSAT suite: http://rsat.ulb.ac.be/rsat. Web site: http://rsat.ulb.ac.be/rsat/retrieve-ensembl-seq_form.cgi. Web services: http://rsat.ulb.ac.be/rsat/web_services/RSATWS.wsdl. Stand-alone distribution: freely available under an academic licence to download from the RSAT web site. The complete manual, a convenient tutorial and demos are available from the RSAT website. Additional help can be found on the RSAT public forum. | bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: Yeast Search for Transcriptional Regulators And Consensus Tracking |
DOI:10.1093/nar/gkv362 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:rsat, nif-0000-31437, OMICS_08097 | https://bio.tools/rsat | https://sources.debian.org/src/rsat/ | SCR_008560 | RSAT | 2026-09-19 12:57:18 | 108 | |||||
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Single Nucleotide Polymorphism Spectral Decomposition (SNPSpD) Resource Report Resource Website 10+ mentions |
Single Nucleotide Polymorphism Spectral Decomposition (SNPSpD) (RRID:SCR_008621) | SNPSpD | analysis service resource, data analysis service, production service resource, service resource | SNPSpD is a method of correcting for non-independance of single nucleotide polymorphisms (SNPs) in linkage disequilibrium (LD) with each other, on the basis of the spectral decomposition (SpD) of matrices of LD between SNP''s. Additionally, output from SNPSpD includes eigenvalues, principal-component coefficients, and factor loadings after varimax rotation, enabling the selection of a subset of SNPs that optimize the information in a genomic region. | bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Queensland Institute of Medical Research |
National Health and MRC Australia 241916 | PMID:14997420 | biotools:snpspd, nif-0000-31985 | https://bio.tools/snpspd | http://genepi.qimr.edu.au/general/daleN/SNPSp | SCR_008621 | Single Nucleotide Polymorphism Spectral Decomposition | 2026-09-19 12:57:18 | 18 | ||||
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Webproanalyst Resource Report Resource Website |
Webproanalyst (RRID:SCR_008348) | analysis service resource, data analysis service, production service resource, service resource | WebProAnalyst provides web-accessible analysis for scanning the quantitative structure-activity relationships in protein families. It searches for a sequence region, whose substitutions are correlated with variations in the activities of a homologous protein set, the so-called activity modulating sites. WebProAnalyst allows users to search for the key physicochemical characteristics of the sites that affect the changes in protein activities. It enables the building of multiple linear regression and neural networks models that relate these characteristics to protein activities. WebProAnalyst implements multiple linear regression analysis, back propagation neural networks and the Structure-Activity Correlation/Determination Coefficient (SACC/SADC). A back propagation neural network is implemented as a two-layered network, one layer as input, the other as output (Rumelhart et al, 1986). WebProAnalyst uses alignment of amino acid sequences and data on protein activity (pK, Km, ED50, among others). The input data are the numerical values for the physicochemical characteristics of a site in the multiple alignment given by a slide window. The output data are the predicted activity values. The current version of WebProAnalyst handles a single activity for a single protein. The SACC/SADC may be defined as an estimate of the strongest multiple correlation between the physicochemical characteristics of a site in a multiple alignment and protein activities. The SACC/SADC coefficient makes possible the calculation of the possible highest correlation achievable for the quantitative relationship between the physicochemical properties of sites and protein activities. The SACC/SADC is a convenient means for an arrangement of positions by their functional significance. WebProAnalyst outputs a list of multiple alignment positions, the respective correlation values, also regression analysis parameters for the relationships between the amino acid physicochemical characteristics at these positions and the protein activity values. | family, functional, activity, alignment, amino acid, homologous, modulating site, neural, physicochemical, propagation, protein, quantitative, region, relationship, scan, sequence, structure, substitution, variation, bio.tools |
is listed by: bio.tools is listed by: Debian |
nif-0000-25212, biotools:webproanalyst | https://bio.tools/webproanalyst | SCR_008348 | Webproanalyst | 2026-09-19 12:57:17 | 0 |
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Welcome to the NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
