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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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SequelQC Resource Report Resource Website 1+ mentions |
SequelQC (RRID:SCR_017279) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool that calculates key statistics and generates publication quality plots for raw PacBio Sequel data. Open source software for analyzing PacBio Sequel raw sequence data. | raw, data, PacBio, Sequel, analysis, sequence, DNA, read, length, plot | NSF Plant Genome Research Program IOS-1744001 | DOI:10.1101/611814 | Free, Freely available, Available for download | SCR_017279 | 2026-09-05 06:28:21 | 2 | |||||||||
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GeneMarkS-T Resource Report Resource Website 100+ mentions |
GeneMarkS-T (RRID:SCR_017648) | data analysis software, data processing software, software application, software resource | Software package for ab initio identification of protein coding regions in RNA transcripts. Algorithm parameters are estimated by unsupervised training which makes unnecessary manually curated preparation of training sets. Sets of assembled eukaryotic transcripts can be analyzed by modified GeneMarkS-T algorithm which part of gene prediction programs GeneMark. | Identification, protein, coding, region, RNA, transcript, gene, discovery, eukaryotic, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Georgia Institute of Technology; Georgia; USA |
NHGRI HG000783 | PMID:25870408 | Restricted | biotools:GeneMarkS-t | https://bio.tools/GeneMarkS-T | SCR_017648 | 2026-09-05 06:28:27 | 172 | ||||||
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Canadian Epigenetics, Environment and Health Research Consortium Network Resource Report Resource Website |
Canadian Epigenetics, Environment and Health Research Consortium Network (RRID:SCR_017491) | consortium, data or information resource, organization portal, portal | Network to connect Canadian epigenetics researchers and expand their reach to broader health research community in Canada and beyond. Curated epigenomics sequence focused on common human diseases. | Curated, epigenomic, sequence, human, disease | is related to: International Human Epigenome Consortium | Canadian Institutes of Health Research (CIHR) ; Genome Canada |
Free, Freely available | SCR_017491 | CEEHRC Network | 2026-09-05 06:28:25 | 0 | ||||||||
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RAMPAGE Resource Report Resource Website 100+ mentions |
RAMPAGE (RRID:SCR_017590) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2021.Web based structural analysis tool for any uploaded PDB file, producing Ramachandran plots, computing dihedral angles and extracting sequence from PDB. Used to visualize dihedral angles ψ against φ of amino acid residues in protein structure. | Ramachandran, plot, analysis, upload, PDB, file, coputing, dihedral, angle, extracting, sequence, protein, amino acid, residue, structure | has parent organization: University of Cambridge; Cambridge; United Kingdom | THIS RESOURCE IS NO LONGER IN SERVICE. | SCR_017590 | 2026-09-05 06:28:26 | 136 | ||||||||||
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AmoebaDB Resource Report Resource Website 1+ mentions |
AmoebaDB (RRID:SCR_017592) | analysis service resource, data or information resource, database, production service resource, service resource | Integrated genomic and functional genomic database for Entamoeba and Acanthamoeba parasites. Contains genomes of three Entamoeba species and microarray expression data for E. histolytica. Integrates whole genome sequence and annotation and includes experimental data and environmental isolate sequences provided by community researchers. | Genomic, functional, database, Entamoeba, Acanthamoeba, parasite, microarray, expression, data, experimental, isolate, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Eukaryotic Pathogen Database Resources |
Department of Health and Human Services ; NIDA ; NIH |
PMID:20974635 | Free, Freely available | biotools:amoebadb, r3d100012457 | https://bio.tools/amoebadb, https://doi.org/10.17616/R3PX9Q | SCR_017592 | 2026-09-05 06:28:26 | 8 | ||||||
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Michigan Imputation Server Resource Report Resource Website 100+ mentions |
Michigan Imputation Server (RRID:SCR_017579) | data access protocol, service resource, software resource, web service | Web server to implement whole genotype imputation workflow for efficient parallelization of computationally intensive tasks. Service for imputation that facilitates access to new reference panels and greatly improves user experience and productivity. Used to find haplotype segments and reference panel of sequenced genomes, assign genotypes at untyped markers, improve genome coverage, facilitate comparison and combination of studies that use different marker panels, increase power to detect genetic association, and guide fine mapping. | Whole, genotype, imputation, workflow, parallelization, task, find, haplotype, segment, reference, panel, sequence, genome, mapping | has parent organization: University of Michigan; Ann Arbor; USA | Austrian Science Fund ; European Community Seventh Framework Programme ; NHGRI HG000376; NHGRI HG007022; NHLBI HL117626; NIA ; NIDA R01 DA037904 |
PMID:27571263 | Restricted | https://github.com/genepi/imputationserver | SCR_017579 | Next Generation Genotype Imputation Service | 2026-09-05 06:28:26 | 196 | ||||||
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Multiple Mapping Method Server Resource Report Resource Website 1+ mentions |
Multiple Mapping Method Server (RRID:SCR_018015) | MMM server | alignment software, data access protocol, data processing software, image analysis software, service resource, software application, software resource, web service | Web server for modeling protein structure by using Multiple Mapping Method. Approach to sequence-to-structure alignment in comparative protein structure modeling. | Modeling protein structure, multiple mapping method, sequence, structure, alignment, comparative protein structure | PMID:16437570 | Free, Freely available | SCR_018015 | Multiple Mapping Method server | 2026-09-05 06:28:29 | 3 | ||||||||
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MUMmer Resource Report Resource Website 500+ mentions |
MUMmer (RRID:SCR_018171) | alignment software, data processing software, image analysis software, software application, software resource | Software package as system for rapidly aligning entire genomes. Alignment tool for DNA and protein sequences. Can align incomplete genomes. | Align, genome, DNA, protein, sequence, , bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite is related to: MUMmerGPU |
NIAID N01 AI15447; NLM R01 LM06845; NSF IIS 9902923 |
PMID:14759262 | Free, Available for download, Freely available | OMICS_14554, biotools:mummer | https://github.com/mummer4/mummer, https://bio.tools/mummer, https://sources.debian.org/src/mummer/ | SCR_018171 | MUMmer4, MUMmer 3.0 | 2026-09-05 06:28:32 | 547 | |||||
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rSeq Resource Report Resource Website 1+ mentions |
rSeq (RRID:SCR_000562) | software resource, software toolkit, source code | A software toolkit for RNA sequence data analysis. It contains programs that cover several aspects of RNA-Seq data analysis such as read quality assessment, reference sequence generation, sequence mapping, and gene and isoform expressions estimations. | rna, sequence, read quality assessment, reference sequence generation, sequence mapping, gene, isoform expressions estimations, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Michigan; Ann Arbor; USA |
Free, Available for download, Freely available, | OMICS_01288, biotools:rseq | https://bio.tools/rseq | SCR_000562 | RNA-Seq Analyzer, rSeq: RNA-Seq Analyzer | 2026-09-05 06:31:10 | 4 | |||||||
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GlycoFragment Resource Report Resource Website 1+ mentions |
GlycoFragment (RRID:SCR_001573) | GlycoFragment | analysis service resource, data analysis service, production service resource, 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 | 2026-09-05 06:31:14 | 1 | |||||||
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DictyOGlyc Resource Report Resource Website 10+ mentions |
DictyOGlyc (RRID:SCR_001600) | DictyOGlyc | analysis service resource, data analysis service, production service resource, 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 | 2026-09-05 06:31:14 | 17 | |||||
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SSCprofiler Resource Report Resource Website 1+ mentions |
SSCprofiler (RRID:SCR_001282) | SSCprofiler | analysis service resource, data analysis service, production service resource, 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 | 2026-09-05 06:31:13 | 5 | ||||||
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ArkDB - Genomes For The Rest of Us Resource Report Resource Website 10+ mentions |
ArkDB - Genomes For The Rest of Us (RRID:SCR_001838) | data or information resource, database | The ArkDB database system aims to provide a comprehensive public repository for genome mapping data from farmed and other animal Species. The system also aims to provide a route in to genomic and other sequence from the initial viewpoint of linkage mapping, RH mapping, physical mapping or - possibly more importantly - QTL mapping data. Sponsors: ArkDB is funded by Biotechnology and Biological Sciences Research Council (BBSRC), UK. Cat, Chicken, Cow, Deer, Duck, Horse, Pig, Quail, Salmon, Sea Bass, Sheep, Turkey, QLT map, Linkage map, RH map, Farm animal, Genome map, Sequence, Mapping | duck, farm animal, cat, chicken, cow, deer, genome map, horse, linkage map, mapping, model organism comparative genomic, pig, qlt map, quail, rh map, salmon, sea bass, sequence, sheep, turkey | has parent organization: Roslin Institute | PMID:11125062 | Free, Freely available | nif-0000-02568, r3d100012788 | SCR_001838 | ArkDB | 2026-09-05 06:31:15 | 22 | |||||||
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Genome Network Platform Resource Report Resource Website 10+ mentions |
Genome Network Platform (RRID:SCR_001737) | GNP | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Integrated database of experiment data generated by participating research institutes and public databases relating to: 1) transcription starting position of human genes in the human genome, 2) conjunction to control region on transcriptional factors and the human genome 3) protein-protein interaction with a central focus on transcription factors organized for use in genome level research. Gene Search is the function to search the integrated database by using keywords and public IDs. The search results can be visualized by: * Genome Explorer : provides annotation of landmarks (genes, transcription start sites, etc.) aligned in accordance with their genome locations. * PPI Network : provides a graphical view of protein-protein interaction (PPI) network from the experimental data generated under the project and the public datasets. * Expression Profile : clusters genes by expression pattern and display the result with heatmap. The function provides genes which have relation of coregulation and anti-coregulation. * Comparison Viewer : This function gives the view to compare the genomic regions between human and mouse homologous genes. The viewer shows the distribution of transcription start sites (TSS) as the way of separable by tissues or time points with other landmarks on genome region. * Gene Stock : This is the function to save the gene list that you are interested until the session is closed. | gene, genome, chip, human, interaction, micro array, protein, protein-protein interaction, qrt-pcr, rat, rna, sequence, short rna, tiling array, transcription, transcription control, transcription factor, transcription starting position, yeast two hybrid, data set, cage, data analysis service |
is listed by: 3DVC has parent organization: National Institute of Genetics; Shizuoka; Japan |
PMID:24927841 | Free, Freely Available | nif-0000-10237 | http://genomenetwork.nig.ac.jp/index_e.html | SCR_001737 | 2026-09-05 06:31:15 | 20 | ||||||
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AutoPSI database of predicted SCOP classifications Resource Report Resource Website |
AutoPSI database of predicted SCOP classifications (RRID:SCR_001923) | data or information resource, database | Searchable database for predicted protein sequences and structures. It has the ability to search through PDB ID, UniProt ID, and descriptive classifiers. | protein, structure, sequence, database, search, uniprot | has parent organization: Ludwig-Maximilians-University; Munich; Germany | Ludwig Maximilians Universitat Munchen | PMID:17932066 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02588 | SCR_001923 | Automated Protein Structure Identification (AutoPSI) database, AutoPSI, AutoPSI Database, Automated Protein Structure Identification database | 2026-09-05 06:31:15 | 0 | ||||||
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PepBank Peptide Database Resource Report Resource Website 10+ mentions |
PepBank Peptide Database (RRID:SCR_002086) | data or information resource, database | A database of peptides based on sequence text mining and public peptide data sources. Only peptides that are 20 amino acids or shorter are stored. Only peptides with available sequences are stored. After submitting a query you can further refine the results using the new heat map retrieval tool to quickly find the entries that are most relevant to you. Text classification helps you find candidate peptides that are related to cancer, cardiovascular diseases, diabetes, apoptosis, angiogenesis and molecular imaging or peptides for which binding data exist. | amino acid, blast search, peptide, sequence, smith-waterman search | PMID:17678535 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20887 | SCR_002086 | PepBank | 2026-09-05 06:31:16 | 34 | ||||||||
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Parasite Databases of Clustered ESTs Resource Report Resource Website 1+ mentions |
Parasite Databases of Clustered ESTs (RRID:SCR_002262) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. These databases were constructed by extracting the organism specific ESTs from dbEST, removing polyA sequences from the ends and trimming 5' and 3' regions with greater than 25% N's in a 20 base pair window. These quality sequences were then aligned using the cap2 program and the consensus sequences thus generated put into a database that is available on the web. A number of parasitic organisms were chosen that have between 3000 and 15000 ESTs. The attempt here is to provide useful information and analyses to the scientific community without curating the results in any way. A total of 55192 ESTs, deposited into dbEST/GenBank, were included in the analyses. The resulting sequences have been clustered into nonredundant gene assemblies and deposited into a relational database that supports a variety of sequence and text searches. This database has been used to compare the gene assemblies using BLAST similarity comparisons to the public protein databases to identify putative genes. Of these new entries, approximately 15%-20% represent putative homologs with a conservative cutoff of p < 10(-9), thus identifying many conserved genes that are likely to share common functions with other well-studied organisms. Gene assemblies were also used to identify strain polymorphisms, examine stage-specific expression, and identify gene families. An interesting class of genes that are confined to members of this phylum and not shared by plants, animals, or fungi, was identified. These genes likely mediate the novel biological features of members of the Apicomplexa and hence offer great potential for biological investigation and as possible therapeutic targets. | est, expression, fungus, gene, animal, apicomplexa, biological, organism, parasitic, phylum, plants, polya, protein, sequence, therapeutic | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20980 | SCR_002262 | PDCEST | 2026-09-05 06:31:17 | 2 | |||||||||
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DBD: Transcription factor prediction database Resource Report Resource Website 10+ mentions |
DBD: Transcription factor prediction database (RRID:SCR_002300) | DBD | data or information resource, database, service resource | Database of predicted transcription factors in completely sequenced genomes. The predicted transcription factors all contain assignments to sequence specific DNA-binding domain families. The predictions are based on domain assignments from the SUPERFAMILY and Pfam hidden Markov model libraries. Benchmarks of the transcription factor predictions show they are accurate and have wide coverage on a genomic scale. The DBD consists of predicted transcription factor repertoires for 930 completely sequenced genomes. | predicted transcription factor, transcription factor, dna-binding domain, proteome, sequence, domain family, protein sequence, genome, prediction |
is listed by: OMICtools is related to: SUPERFAMILY is related to: Pfam has parent organization: MRC Laboratory of Molecular Biology |
PMID:18073188 PMID:16381970 |
Acknowledgement requested | nif-0000-02726, OMICS_00531 | SCR_002300 | DNA-binding domain | 2026-09-05 06:31:17 | 10 | ||||||
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Ligand-Gated Ion Channel Database Resource Report Resource Website 1+ mentions |
Ligand-Gated Ion Channel Database (RRID:SCR_002418) | LGICdb | data or information resource, database | Database providing access to information about transmembrane proteins that exist under different conformations, with three primary subfamilies: the cys-loop superfamily, the ATP gated channels superfamily, and the glutamate activated cationic channels superfamily. Due to the lack of evolutionary relationship, these three superfamilies are treated separately. It currently contains 554 entries of ligand-activated ion channel subunits. In this database one may find: the nucleic and proteic sequences of the subunits. Multiple sequence alignments can be generated, and some phylogenetic studies of the superfamilies are provided. Additionally, the atomic coordinates of subunits, or portion of subunits, are provided when available. Redundancy is kept to a minimum, i.e. one entry per gene. Each entry in the database has been manually constructed and checked by a researcher of the field in order to reduce the inaccuracies to a minimum. NOTE: This database is not actively maintained anymore. People should not consider it as an up-to-date trustable resource. For any new work, they should consider using alternative sources, such as UniProt, Ensembl, Protein Databank etc. | equilibrium, extracellular, gabaa, gated, gene, genetics, 3d model, alignment, anionic, atomic, atp, cationic, cellular, molecular, channel, compartment, computation, conformation, coordinate, cys-loop, glutamate, glycine, histamine, homologous, ion, ion channel, ligand, membrane, nicotinic, nucleic acid, phylogenetic, pore, portion, proteic, nucleic acid, protein, phylogeny, receptor, segment, sequence, sequence data, serotonin, subunit, superfamily, transmembrane |
is listed by: re3data.org has parent organization: European Bioinformatics Institute |
College of France; Paris; France ; Centre National de la Recherche Scientifique ; European Union ; Biotech and Biomed contracts ; French Ministry of Higher Education and Research ; Institut Pasteur |
PMID:16381861 PMID:11125117 |
nif-0000-00037, r3d100010796 | https://doi.org/10.17616/R3Q90D | SCR_002418 | LGIC Database | 2026-09-05 06:31:17 | 1 | |||||
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object-oriented Transcription Factors Database Resource Report Resource Website 1+ mentions |
object-oriented Transcription Factors Database (RRID:SCR_002435) | data or information resource, database | ooTFD (object-oriented Transcription Factors Database) is a successor to TFD, the original Transcription Factors Database. This database is aimed at capturing information regarding the polypeptide interactions which comprise and define the properties of transcription factors. ooTFD contains information about transcription factor binding sites, as well as composite relationships within transcription factors, which frequently occur as multisubunit proteins that form a complex interface to cellular processes outside the transcription machinery through protein-protein interactions. ooTFD contains information represented in TFD but also allows the representation of containment, composite, and interaction relationships between transcription factor polypeptides. It is designed to represent information about all transcription factors, both eukaryotic and prokaryotic, basal as well as regulatory factors, and multiprotein complexes as well as monomers. | eukaryotic, expression, factor, gene, basal, binding site, biochemical, biology, cellular, complex, genome, genomic, information, interaction, molecule, monomer, multisubunit, nucleotide sequences, transcriptional regulator sites, transcription factors, object, polypeptide, process, prokaryotic, property, protein, protein-protein interaction, regulatory, sequence, transcription | has parent organization: IFTI-Mirage | PMID:10592257 PMID:9847215 PMID:9399874 |
Free, Freely available | nif-0000-21303 | SCR_002435 | ooTFD | 2026-09-05 06:31:17 | 2 |
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