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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Mammalian Gene Collection Resource Report Resource Website 10+ mentions |
Mammalian Gene Collection (RRID:SCR_007024) | MGC | cell repository, biomaterial supply resource, material resource | NIH initiative project to provide full-length open reading frame (FL-ORF) clones for human, mouse, and rat genes, cow. MGC cDNA clones were obtained by screening of cDNA libraries, by transcript-specific RT-PCR cloning, and by DNA synthesis of cDNA inserts. All MGC sequences are deposited in GenBank and clones can be purchased from distributors of IMAGE consortium. With conclusion of MGC project in March 2009, GenBank records of MGC sequences will be frozen, without further updates. Since definition of what constitutes full-length coding region for some of genes and transcripts for which they have MGC clones will likely change in future, users planning to order MGC clones will need to monitor for these changes. Users can make use of genome browsers and gene-specific databases, such as the UCSC Genome browser, NCBI's Map Viewer, and Entrez Gene, to view relevant regions of genome (browsers) or gene-related information (Entrez Gene). | cell line, cdna, frozen, clone, vector, gene, open reading frame, sequence, expressed sequence tag, bio.tools, FASEB list |
is listed by: One Mind Biospecimen Bank Listing is listed by: bio.tools is listed by: Debian is related to: One Mind Biospecimen Bank Listing is related to: NIDDK Information Network (dkNET) is related to: ATCC is related to: GenBank is related to: Invitrogen Clones is related to: Open Biosystems is related to: Zebrafish Gene Collection has parent organization: National Cancer Institute |
NIH Blueprint for Neuroscience Research | Free, Freely available | biotools:mammalian_gene_collection, nif-0000-00195 | https://bio.tools/mammalian_gene_collection | SCR_007024 | Mammalian Gene Collection | 2026-07-27 09:32:43 | 46 | |||||
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BioRep Resource Report Resource Website 100+ mentions |
BioRep (RRID:SCR_004907) | BioRep | cell repository, biomaterial supply resource, material resource | Offer biorepository services to public and private research institutes, to the highest standards of quality and safety with the aim of contributing to the advancement of medical research and scientific discovery. The BioRep Cell Repository establishes, maintains and distributes cell line cultures as well as DNA derived from these cultures. The scientific and business affiliation between BioRep and Coriell allows access to more than a million types of cell vials, stored in liquid nitrogen. Cells that have been stored for nearly 50 years, are still viable and available for research purposes today. Thanks to an exclusive agreement with the Coriell Institute for Medical Research, the oldest and largest biorepository of the world, BioRep is specialized in cell lines preparation, in nucleic acid extraction and long term storage in liquid nitrose (-196 degrees C) and in refrigerators (-80 degrees C) of any kind of biosamples, using procedures and standards developed by the Coriell in over 50 years of activity. BioRep and Coriell together constitute one of the few Global Biorepository able to serve the pharmaceutical industries for world wide clinical trials. BioRep facility is specifically designed to give the utmost efficiency and security by implementing Coriell procedures and standards. The BioRep Tissue Repository provides safe and secure storage of tissue specimens as required for medical research and scientific investigation. All tissues are preserved with the most current preservation techniques and processes. In addition to the storage service, BioRep provides Cell Biology, Molecular Biology, Microbiology services developed in ISO 9001:2008 certified laboratories. | chromosome analysis, dhplc analysis, methylation, genotyping, gender analysis, sequencing service, nucleic acid isolation, catalog, cell line, dna, cell, tissue, frozen, liquid nitrogen, vapor nitrogen, refrigerator, fixed, paraffin embedded, slide, cryogenic, paraffin block, cryopreserved, molecular biology, microbiology, cytogenetics, media preparation, tissue microarray, cell array, frozen array, cell biology, research, transplantation, custom, blood, tissue, ebv transformed lymphoblast culture, fibroblast cell culture, nucleic acid, sequence, mycoplasma, karyotype |
is listed by: One Mind Biospecimen Bank Listing is related to: Coriell Institute for Medical Research |
Public: offer biorepository services to public and private research institutes, To the highest standards of quality and safety. BioRep is one of the few ''''Global Biorepository'''' able to serve the pharmaceutical industries for world wide clinical trials. | nlx_87504 | http://www.biorep.it/eng/ | SCR_004907 | 2026-07-27 09:32:09 | 166 | |||||||
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TMHMM Server Resource Report Resource Website 1000+ mentions |
TMHMM Server (RRID:SCR_014935) | web application, software resource | Web application for the prediction of transmembrane helices in proteins using Hidden Markov Models. FASTA formatted sequences can be uploaded via file or copy-paste, and output can be formatted as extensive with graphics, extensive without graphics, or one line per protein. Submissions are limited to 10,000 sequences and 4,000,000 amino acids - each sequence is limited to no more than 8,000 amino acids. | sequence, amino acid, web application, transmembrane helices, hidden markov model, fasta | Open source | SCR_014935 | TMHMM Server v 2.0 | 2026-07-27 09:34:46 | 1872 | ||||||||||
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ProP Server Resource Report Resource Website 50+ mentions |
ProP Server (RRID:SCR_014936) | web application, software resource | Web application which predicts arginine and lysine propeptide cleavage sites in eukaryotic protein sequences using an ensemble of neural networks. Furin-specific prediction is the default. It is also possible to perform a general proprotein convertase prediction. | web application, prediction, arginine, lysine, cleavage, propeptide, eukaryotic, protein, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1093/protein/gzh013 | Open source | biotools:prop, BioTools:prop | https://bio.tools/prop, https://bio.tools/prop, https://bio.tools/prop | SCR_014936 | ProP, ProP 1.0 Server, ProP 1.0 | 2026-07-27 09:34:46 | 75 | ||||||
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Composition Profiler Resource Report Resource Website 10+ mentions |
Composition Profiler (RRID:SCR_014630) | web application, software resource | Web tool for discovery and visualization of differences in amino acid composition. Two samples of amino acid sequences serve as input and a bar chart composed of twenty data points is output. | web tool, web application, amino acid, amino acid composition, sequence, bar chart, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:17578581 | Source code available, Acknowledgement requested | biotools:composition_profiler | https://bio.tools/composition_profiler | SCR_014630 | 2026-07-27 09:34:44 | 32 | |||||||
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GlycoFragment Resource Report Resource Website 1+ mentions |
GlycoFragment (RRID:SCR_001573) | GlycoFragment | analysis service resource, service resource, data analysis service, production service resource | Service that calculates and displays the main fragments (Band C-, Z- and Y-, A- and X-ions) of oligosaccharides that should occur in MS-spectra. The extended ASCII nomenclature as recommended by IUPAC is used to input the sequence of complex oligosaccharides. However, some additional input rules have to be fulfilled. In case only the topology and composition of the oligosaccharide is known, a simpler way to input carbohydrate sequences is possible. Since the hydroxyl groups of synthetic carbohydrates are often the are protected they have included a way to indicate if sugar residue are persubstituted. Please have a look at the examples of valid input structures. | fragment, mass spectrometry, carbohydrate, sequence, oligosaccharide, mass spectrometry-spectra, structure, ion | has parent organization: glycosciences.de | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152886 | SCR_001573 | GlycoFragments, Sugar Fragmentation | 2026-07-27 09:31:15 | 1 | |||||||
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DictyOGlyc Resource Report Resource Website 10+ mentions |
DictyOGlyc (RRID:SCR_001600) | DictyOGlyc | analysis service resource, service resource, data analysis service, production service resource | Server that produces neural network predictions for GlcNAc O-glycosylation sites in Dictyostelium discoideum proteins. | glcnac glycosylation site, neural network, o-glycosylation, prediction, proteome, glycoprotein, glcnac, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: CBS Prediction Servers |
Deutscher Akademischer Austauschdienst ; HspII/AUFE ; Macquarie University International Postgraduate Research Award ; Australian Research Council ; National Health and MRC ; Danish National Research Foundation |
PMID:10521537 | Free, Freely available | nlx_153856, biotools:dictyoglyc | https://bio.tools/dictyoglyc | SCR_001600 | 2026-07-27 09:31:15 | 14 | |||||
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SSCprofiler Resource Report Resource Website 1+ mentions |
SSCprofiler (RRID:SCR_001282) | SSCprofiler | analysis service resource, service resource, data analysis service, production service resource | Tool which can be used to identify novel miRNA gene candidates in the human genome. | microrna, gene, genome, sequence, structure, conservation |
is listed by: OMICtools has parent organization: Institute of Molecular Biology and Biotechnology; Heraklion; Greece |
PMID:19324892 | Free, Freely available | OMICS_02055 | SCR_001282 | Sequence Structure and Conservation profiler | 2026-07-27 09:31:10 | 3 | ||||||
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Coddle-Codons Optimized to Discover Deleterious LEsions Resource Report Resource Website 10+ mentions |
Coddle-Codons Optimized to Discover Deleterious LEsions (RRID:SCR_003003) | CODDLE | analysis service resource, service resource, data analysis service, production service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Web-accessible program that identifies the region(s) of a user-selected gene and of its coding sequence (CDS) where the anticipated point mutations are most likely to result in deleterious effects on the gene's function. CODDLe separately handles 1) the prediction of changes which should truncate the protein and destabilize the RNA - nonsense changes and splice junction changes, and 2) the prediction of missense changes which should alter function of the gene product - those in conserved amino acid blocks in the CDS. Because the region(s) identified will be PCR amplified by the user and that amplicon will be used for polymorphism discovery, the application delivers primer pairs selected by Primer3 (Steve Rozen, Helen J. Skaletsky (1996,1997,1998)Primer3.) After selecting a primer pair, CODDLe returns a window with the selected amplicon and tabulates the effects of all possible polymorphisms which could be detected in that amplicon. CODDLe will not identify the regions of a gene where polymorphisms are most likely to be discovered. Others have shown that naturally occurring SNPs are found more often in the untranslated regions of a gene. | codon, deleterious lesion, gene, coding, sequence, mutation, primer, protein sequence, cdna, sequence alignment, coding sequence |
is listed by: 3DVC has parent organization: Fred Hutchinson Cancer Center |
DOE ; Office of Energy Research |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30262 | SCR_003003 | Choosing codons to Optimize Discovery of Deleterious Lesions, Codons Optimized to Discover Deleterious LEsions | 2026-07-27 09:31:38 | 16 | ||||||
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BiSearch: Primer Design and Search Tool Resource Report Resource Website 50+ mentions |
BiSearch: Primer Design and Search Tool (RRID:SCR_002980) | BiSearch | analysis service resource, service resource, data analysis service, production service resource | BiSearch is a primer-design algorithm for DNA sequences. It may be used for both bisulfite converted as well as for original not modified sequences. You can search various genomes with the designed primers to avoid non-specific PCR products by our fast ePCR method. This is especially recommended when primers are designed to amplify the highly redundant bisulfite treated sequences. It has the unique property of analyzing the primer pairs for mispriming sites on the bisulfite-treated genome and determines potential non-specific amplification products with a new search algorithm. The options of primer-design and analysis for mispriming sites can be used sequentially or separately, both on bisulfite-treated and untreated sequences. In silico and in vitro tests of the software suggest that new PCR strategies may increase the efficiency of the amplification. | dna, sequence, primer, design, algorithm, analysis, priming, bisulfite, genome, amplification, in vitro, in silico, amplification, epcr, cytosines | has parent organization: Hungarian Academy of Sciences; Budapest; Hungary | PXE International Inc. GVOP-3.1.1-2004-05-0143/3.0; Boolyai Janos Scholarship ; OTKA T34131; OTKA D42207 |
PMID:17022803 PMID:15653630 |
nif-0000-30170 | SCR_002980 | 2026-07-27 09:31:38 | 50 | |||||||
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TFSEARCH: Searching Transcription Factor Binding Sites Resource Report Resource Website 100+ mentions |
TFSEARCH: Searching Transcription Factor Binding Sites (RRID:SCR_004262) | analysis service resource, service resource, data analysis service, production service resource | The TFSEARCH searches highly correlated sequence fragments against TFMATRIX transcription factor binding site profile database in the "TRANSFAC" databases developed at GBF-Braunschweig, Germany. The TFSEARCH program was written by Yutaka Akiyama (Kyoto University, currently at RWCP) in 1995. | vertebrate, arthropod, plant, yeast, dna, sequence, FASEB list |
is related to: TFFACTOR has parent organization: Computational Biology Research Center Core Facility |
PMID:9399875 | nlx_27602 | http://www.cbrc.jp/research/db/TFSEARCH.html | SCR_004262 | TFSEARCH: DNA Transcription Factor Binding Site Prediction, Transcriptional Factor Search, TFSEARCH | 2026-07-27 09:31:58 | 214 | |||||||
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MG-RAST Resource Report Resource Website 1000+ mentions |
MG-RAST (RRID:SCR_004814) | MG RAST | analysis service resource, service resource, data analysis service, production service resource | An automated analysis platform for metagenomes providing quantitative insights into microbial populations based on sequence data. The server primarily provides upload, quality control, automated annotation and analysis for prokaryotic metagenomic shotgun samples. | metagenome, base pair, sequence, phylogenetic, functional analysis, data sharing, metadata, protein, micro biome, analysis platform, bio.tools |
is listed by: OMICtools is listed by: Human Microbiome Project is listed by: Debian is listed by: bio.tools has parent organization: Argonne National Laboratory |
NIAID contract HHSN272200900040C; DOE contract DE-AC02-06CH11357 |
PMID:18803844 | Acknowledgement requested, Public, Account required | OMICS_01456, biotools:mg-rast | http://metagenomics.nmpdr.org, https://bio.tools/mg-rast | SCR_004814 | The Metagenomics RAST server, Metagenomics RAST, MG-RAST - metagenomics analysis server | 2026-07-27 09:32:08 | 1137 | ||||
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Human Splicing Finder Resource Report Resource Website 500+ mentions |
Human Splicing Finder (RRID:SCR_005181) | HSF | analysis service resource, service resource, data analysis service, production 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 | 2026-07-27 09:32:13 | 963 | |||||
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PRED-CLASS Resource Report Resource Website |
PRED-CLASS (RRID:SCR_006216) | PRED-CLASS | analysis service resource, service resource, data analysis service, production service resource | A system of cascading neural networks that classifies any protein, given its amino acid sequence alone, into one of four possible classes: membrane, globular, fibrous, mixed. | classification, protein, fibrous, globular, protein class, membrane, sequence, algorithm, protein classification, neural network, transmembrane, genome annotation, genome-wide analysis |
is related to: DAM-Bio has parent organization: University of Athens Biophysics and Bioinformatics Laboratory |
European Union ERBFMRXCT960019 | PMID:11455609 | nlx_151762 | SCR_006216 | PRED-CLASS - Classification of proteins into one of four possible classes | 2026-07-27 09:32:29 | 0 | ||||||
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ProbeExplorer Resource Report Resource Website |
ProbeExplorer (RRID:SCR_007116) | ProbeExplorer | analysis service resource, service resource, data analysis service, production service resource | Probe Explorer is an open access web-based bioinformatics application designed to show the association between microarray oligonucleotide probes and transcripts in the genomic context, but flexible enough to serve as a simplified genome and transcriptome browser. Coordinates and sequences of the genomic entities (loci, exons, transcripts), including vector graphics outputs, are provided for fifteen metazoa organisms and two yeasts. Alignment tools are used to built the associations between Affymetrix microarrays probe sequences and the transcriptomes (for human, mouse, rat and yeasts). Search by keywords is available and user searches and alignments on the genomes can also be done using any DNA or protein sequence query. Platform: Online tool | bioinformatics, microarray, oligonucleotide probe, transcript, genomic, genome, transcriptome, alignment, affymetrix, probe sequence, dna, protein, sequence, statistical analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of Salamanca; Salamanca; Spain |
Open unspecified license - Free for academic use | nlx_149275 | SCR_007116 | Probe Explorer | 2026-07-27 09:32:44 | 0 | |||||||
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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, service resource, data analysis service, production 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 | 2026-07-27 09:33:03 | 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, service resource, data analysis service, production 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) | 2026-07-27 09:33:13 | 1 | |||||
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Isofinder: Isochore Computational Prediction Resource Report Resource Website |
Isofinder: Isochore Computational Prediction (RRID:SCR_008342) | analysis service resource, service resource, data analysis service, production service resource | Isofinder is an algorithm running on the web able to predict isochores at the sequence level. Isochores are long genome segments homogeneous in G+C. The algorithm works by moving a sliding pointer from left to right along the DNA sequence and computing the mean G+C values to the left and to the right of the pointer at each point. Additionally, the program checks whether this significance exceeds a probability threshold. If so, the sequence is cut at this point into two subsequences; otherwise, the sequence remains undivided. The procedure continues recursively for each of the two resulting subsequences created by each cut. This leads to the decomposition of a chromosome sequence into long homogeneous genome regions (LHGRs) with well-defined mean G+C contents, each significantly different from the G+C contents of the adjacent LHGRs. Most LHGRs can be identified with Bernardi''s isochores, given their correlation with biological features such as gene density, SINE and LINE (short, long interspersed repetitive elements) densities, recombination rate or single nucleotide polymorphism variability. The resulting isochore maps are available at http://bioinfo2.ugr.es/isochores/, and also at the UCSC Genome Browser (http://genome.cse.ucsc.edu/). Sponsors: Isofinder is funded by Universidad de Granada, Spain. | algorithm, chromosome, dna, genome, heterogeneous, homogeneous, isochore, segment, sequence, single nucleotide polymorphism, snp, statistic | has parent organization: University of Granada; Granada; Spain | nif-0000-25208 | SCR_008342 | Isofinder | 2026-07-27 09:33:04 | 0 | |||||||||
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Seq-Gen Resource Report Resource Website 100+ mentions |
Seq-Gen (RRID:SCR_014934) | software application, simulation software, software resource | Software program that simulates the evolution of nucleotide or amino acid sequences along a phylogeny using common models of the substitution process. A range of models of molecular evolution are implemented, including the general reversible model. State frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree. | simulator, simulation software, molecular evolution, nucleotide, amino acid, sequence, phylogeny, phylogenetic tree |
is listed by: Debian is listed by: OMICtools has parent organization: University of Edinburgh; Scotland; United Kingdom |
Wellcome Trust ; BBSRC ; Fogarty ; The Royal Society |
DOI:10.1093/bioinformatics/13.3.235 | Available for download | OMICS_15373 | https://sources.debian.org/src/seq-gen/ | SCR_014934 | 2026-07-27 09:34:50 | 155 | ||||||
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Manipulate and Display a DNA Sequence Resource Report Resource Website |
Manipulate and Display a DNA Sequence (RRID:SCR_013470) | Manipulate and Display a DNA Sequence | analysis service resource, service resource, data analysis service, production service resource | A software tool that allows users to input a DNA (or RNA) sequence and obtain its inverse, complement or inverse complement. The program can also be used to display a DNA sequence and its complement in double-stranded format. Functions after users paste a DNA sequence into the upper text box, then click the appropriate button to place a manipulated form of the sequence in the lower text box. | dna sequence, dna, rna, sequence, inverse, complement, inverse complement, base number | has parent organization: Colorado State University; Colorado; USA | nif-0000-31779 | SCR_013470 | Manipulate Display a DNA Sequence | 2026-07-27 09:34:25 | 0 |
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