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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ProbeExplorer Resource Report Resource Website |
ProbeExplorer (RRID:SCR_007116) | ProbeExplorer | analysis service resource, data analysis service, production service resource, 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 | 2026-08-29 11:29:56 | 0 | |||||||
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Tetraodon nigroviridis Database Resource Report Resource Website |
Tetraodon nigroviridis Database (RRID:SCR_007123) | data or information resource, database | This database have been funded by the National Human Genome Research Institute (NHGRI) to produce shotgun sequence of the Tetraodon nigriviridis genome. The strategy involves Whole Genome Shotgun (WGS) sequencing, in which sequence from the entire genome is generated. Whole genome shotgun libraries were prepared from Tetraodon genomic DNA obtained from the laboratory of Jean Weissenbach at Genoscope. Additional sequence data of approximately 2.5X coverage of Tetraodon has also been generated by Genoscope in plasmid and BAC end reads. Broad and Genoscope intend to pool their data and generate whole genome assemblies. Tetraodon nigroviridis is a freshwater pufferfish of the order Tetraodontiformes and lives in the rivers and estuaries of Indonesia, Malaysia and India. This species is 20-30 million years distant from Fugu rubripes, a marine pufferfish from the same family. The gene repertoire of T. nigroviridis is very similar to that of other vertebrates. However, its relatively small genome of 385 Mb is eight times more compact than that of human, mostly because intergenic and intronic sequences are reduced in size compared to other vertebrate genomes. These genome characteristics along with the large evolutionary distance between bony fish and mammals make Tetraodon a compact vertebrate reference genome - a powerful tool for comparative genetics and for quick and reliable identification of human genes. | estruary, evolutionary, fish, freshwater, fugu rubripes, gene, genetic, bac, bony, distance, dna, genome, genomic, human, intergenic, intronic, nigriviridis, plasmid, pufferfish, river, sequence, sequencing, shotgun, specie, tetraodon, tetraodontiformes, vertebrate | nif-0000-20998 | SCR_007123 | TND | 2026-08-29 11:29:49 | 0 | ||||||||||
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Yeast Intron Database Resource Report Resource Website 1+ mentions |
Yeast Intron Database (RRID:SCR_007144) | Yeast Intron Database | data or information resource, database | Database of information about the spliceosomal introns of the yeast Saccharomyces cerevisiae. Listed are known spliceosomal introns in the yeast genome and the splice sites actually used are documented. Through the use of microarrays designed to monitor splicing, they are beginning to identify and analyze splice site context in terms of the nature and activities of the trans-acting factors that mediate splice site recognition. In version 3.0, expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors is included. These data are displayed on each intron page for browsing and can be downloaded for other types of analysis. | intron, spliceosomal, splicing, genome, intron splice signal, sequence, splice site |
is listed by: OMICtools has parent organization: University of California at Santa Cruz; California; USA |
W. M. Keck Foundation ; Packard Foundation ; NIH |
PMID:11988574 | The community can contribute to this resource | nif-0000-03649, OMICS_01890 | http://www.cse.ucsc.edu/research/compbio/yeast_introns.html | SCR_007144 | Ares lab Yeast Intron Database | 2026-08-29 11:29:49 | 2 | ||||
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Protein Classification Benchmark Collection Resource Report Resource Website 10+ mentions |
Protein Classification Benchmark Collection (RRID:SCR_007561) | data or information resource, database | It was created in order to create standard datasets on which the performance of machine learning methods can be compared. The collection contains datasets of sequences and structures, each subdivided into positive/negative training/test sets. Such a subdivision is called a classification task. Typical tasks include the classification of structural domains in the SCOP and CATH databases based on their sequences, as fell as various functional and taxonomic classification tasks. Running a performance evaluation test on an entire database can include many different classification tasks. These ensembles of classification tasks are encoded in a simple matrix format - called the cast matrix or membership table - that specifies the role of each sequence (or structure) in the different calculations. Each column of this matrix is a subdivision of the objects (rows) into positive/negative training/test sets. Typically, a database record contains such an ensemble of classification tasks, encoded in a single cast matrix. In addition, there is a collection of distance matrices that contain an all vs. all comparison of the datasets using methods as BLAST, Smith-Waterman, 3D-comparisons etc. Evaluation of a method on a given database consists of calculating a performance measure such as a receiver operating curve (ROC) AUC value. Results of evaluation are deposited along with the data, each dataset is evaluated at least by one classification method, such as 1NN (nearest neighbour) or SVM (support vector machines), ANN (artificial neural networks), RF (random forests) etc.. There are small datasets meant for program developers, as well as downloadable programs for various classification algorithms. | classificaiton, machine learning, sequence, standard, standard dataset, structure, technology | nif-0000-02600 | SCR_007561 | Benchmark | 2026-08-29 11:30:00 | 26 | ||||||||||
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CMKB Resource Report Resource Website 1+ mentions |
CMKB (RRID:SCR_007229) | CMKB | data or information resource, database | It is a database of keys facts about proteins, families, and complexes involved in cell migration. This ongoing project provides a large amount of automated and curated data, collected from numerous online resources that are updated monthly. These data include names, synonyms, sequence information, summaries, CMC research data, reagents, structures, as well as protein family and complex details. CMKB''s ultimate goal is to create a database that will enable the cell migration community to conveniently access significant information about molecules of interest. This will also serve as a stepping stone to pathway analysis and demonstrate how these molecules coordinate with one another during cell adhesion and movement. Sponsors: This resource is supported by the Cell Migration Consortium. | cell, migration, knowledgebase, database, protein, family, data, sequence, synonyms, research, reagent, structure, protein, molecule, interest, pathway, adhesion, movement | nif-0000-30312 | SCR_007229 | Cell Migration Knowledgebase, The Cell Migration Knowledgebase | 2026-08-29 11:29:50 | 1 | |||||||||
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GENCODE Resource Report Resource Website 5000+ mentions Rating or validation data |
GENCODE (RRID:SCR_014966) | data or information resource, dataset, portal, project portal | Human and mouse genome annotation project which aims to identify all gene features in the human genome using computational analysis, manual annotation, and experimental validation. | human, mouse, genome, annotation, sequence, gene features, bio.tools |
is listed by: Debian is listed by: bio.tools is affiliated with: ENCODE |
NHGRI 5U54HG004555; Wellcome Trust WT098051 |
PMID:22955987 | Free | biotools:GENCODE | https://bio.tools/GENCODE | SCR_014966 | ENCODE | 2026-08-29 11:28:44 | 8811 | |||||
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Center for Computational Biology at JHU Resource Report Resource Website 1+ mentions |
Center for Computational Biology at JHU (RRID:SCR_016680) | CCB at JHU | data or information resource, organization portal, portal | Center for Computational Biology as a joint research center in the McKusick-Nathans Institute of Genetic Medicine, spanning the School of Medicine, the Whiting School of Engineering, the Bloomberg School of Public Health, and the Krieger School of Arts & Sciences. Multidisciplinary center dedicated to research on genomics, genetics, DNA sequencing technology, and computational methods for DNA and RNA sequence analysis. | center, computational, biology, genomics, genetics, DNA, RNA, sequence, technology, analysis |
has parent organization: Johns Hopkins University; Maryland; USA is parent organization of: Centrifuge Classifier |
SCR_016680 | CCB at Johns Hopkins University, CCB at JHU, Center for Computational Biology at JHU, Center for Computational Biology at Johns Hopkins University | 2026-08-29 11:28:51 | 1 | |||||||||
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tbl2asn Resource Report Resource Website 10+ mentions |
tbl2asn (RRID:SCR_016636) | data processing software, software application, software resource | Software tool as a command-line program that automates the creation of sequence records for submission to GenBank. Records need no additional manual editing before submission. | command, line, program, automate, creation, sequence, record, submit, data, GenBank | has parent organization: NCBI | Free, Freely available | SCR_016636 | 2026-08-29 11:28:57 | 11 | ||||||||||
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Gene-conservation-informed-contig-alignment Resource Report Resource Website 1+ mentions |
Gene-conservation-informed-contig-alignment (RRID:SCR_017617) | GCICA | data processing software, software application, software resource | Software tool for separation haplotigs from genome assembly. Method to separate haplotigs based on sequence similarity. | Separation, haplotig, genome, assembly, sequence, similarity | Free, Available for download, Freely available | SCR_017617 | 2026-08-29 11:28:59 | 1 | ||||||||||
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TPA Resource Report Resource Website 1+ mentions |
TPA (RRID:SCR_003593) | TPA | data or information resource, database | Database designed to capture experimental or inferential results that support submitter-provided annotation for sequence data that the submitter did not directly determine but derived from GenBank primary data. Records are divided into two categories: * TPA:experimental: Annotation of sequence data is supported by peer-reviewed wet-lab experimental evidence. * TPA:inferential: Annotation of sequence data by inference (where the source molecule or its product(s) have not been the subject of direct experimentation) TPA records are retrieved through the Nucleotide Database and feature information on the sequence, how it was cataloged, and proper way to cite the sequence information. | gene, gene expression, nucleotide sequence, annotation, sequence |
is listed by: re3data.org is related to: GenBank is related to: NCBI Protein Database is related to: NCBI Nucleotide has parent organization: NCBI |
PMID:16901214 | nlx_157738, r3d100010506 | https://doi.org/10.17616/R3KS4H | SCR_003593 | Third Party Annotation, NCBI TPA, NCBI Third Party Annotation | 2026-08-29 11:29:23 | 4 | ||||||
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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, data analysis service, production service resource, 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 | 2026-08-29 11:29:31 | 216 | |||||||
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MG-RAST Resource Report Resource Website 1000+ mentions |
MG-RAST (RRID:SCR_004814) | MG RAST | analysis service resource, data analysis service, production service resource, 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 | 2026-08-29 11:29:29 | 1165 | ||||
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Human Splicing Finder Resource Report Resource Website 1000+ mentions |
Human Splicing Finder (RRID:SCR_005181) | HSF | analysis service resource, data analysis service, production service resource, service resource | Software tool to help study pre-mRNA splicing and to better understand intronic and exonic mutations leading to splicing defects. To calculate the consensus values of potential splice sites and search for branch points, new algorithms were developed. Furthermore, they have integrated all available matrices to identify exonic and intronic motifs, as well as new matrices to identify hnRNP A1, Tra2-? and 9G8. | splicing, mutation, splicing signal, sequence, transcript, nucleotide, exon, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Ensembl has parent organization: National Institute of Health and Medical Research; Rennes; France |
PMID:19339519 | Acknowledgement requested | biotools:human_splicing_finder, OMICS_00176 | https://bio.tools/human_splicing_finder | http://www.umd.be/HSF/ | SCR_005181 | 2026-08-29 11:29:40 | 1009 | |||||
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EMBOSSMatcher Resource Report Resource Website 10+ mentions |
EMBOSSMatcher (RRID:SCR_017252) | alignment software, data access protocol, data processing software, image analysis software, software application, software resource, web service | Software tool for pairwise sequence alignment. Identifies local similarities in two input sequences. One of EMBL-EBI search and sequence analysis tools. | pairwise, sequence, alignment, identify, local, similarity, two, input, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools |
EMBL | PMID:30976793 | Free, Freely available | biotools:ebi_search | https://bio.tools/ebi_search | SCR_017252 | EMBOSS Matcher, emboss_matcher, EMBOSS_Matcher | 2026-08-29 11:25:31 | 16 | |||||
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Juicer Resource Report Resource Website 100+ mentions |
Juicer (RRID:SCR_017226) | data analysis software, data processing software, software application, software resource | Software platform for analyzing kilobase resolution Hi-C data. Open source tool for analyzing terabase scale Hi-C datasets. Allowes to transform raw sequence data into normalized contact maps. | analysis, kilobase, resolution, Hi-C, data, terabase, dataset, transform, raw, sequence, normalized, contact, map | has parent organization: Baylor College of Medicine; Houston; Texas | Cancer Prevention Research Institute of Texas ; Google Research Award ; IBM University Challenge Award ; McNair Medical Institute Scholar Award ; NHGRI HG003067; NHGRI HG006193; NHLBI U01 HL130010; NIH Office of the Director DP2 OD008540; NSF PHY-1427654; NVIDIA Research Center Award ; PD Soros Fellowship ; President Early Career Award in Science and Engineering ; Welch Foundation |
PMID:27467249 | Free, Available for download, Freely available | SCR_017226 | 2026-08-29 11:25:32 | 119 | ||||||||
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PIRATE Resource Report Resource Website 10+ mentions |
PIRATE (RRID:SCR_017265) | data analysis software, data processing software, software application, software resource | Software pangenomics toolbox for clustering diverged orthologues in bacteria. Used to identify and classify orthologous gene families in bacterial pangenomes over wide range of sequence similarity thresholds. | Pangenome, clustering, genomics, bacteria, orthologue, gene, sequence, amino acid, nucleotide, dataset, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/598391 | Free, Available for download, Freely available | biotools:PIRAtE | https://bio.tools/PIRATE | SCR_017265 | Pangenome Iterative Refinement And Threshold Evaluation | 2026-08-29 11:25:32 | 23 | ||||||
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RepeatFiller Resource Report Resource Website 10+ mentions |
RepeatFiller (RRID:SCR_017414) | alignment software, data processing software, image analysis software, software application, software resource | Software tool to incorporate newly detected repeat overlapping alignments into pairwise alignment chains. It only aligns local genomic regions that are bounded by colinear aligning blocks, as provided in chains, which makes it feasible to consider all seeds including those that overlap repetitive regions. Used to improve genome alignments by incorporating previously undetected local alignments between repetitive sequences. | Repeat, overlapping, alignment, pairwise, chain, local, genomic, region, colinear, block, sequence, undetected, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Max Planck Institute of Molecular Cell Biology and Genetics; Dresden; Germany |
DOI:10.1101/696922 | Free, Freely available | biotools:RepeatFiller, BioTools:RepeatFiller | https://bio.tools/RepeatFiller, https://bio.tools/RepeatFiller, https://bio.tools/RepeatFiller | SCR_017414 | 2026-08-29 11:25:59 | 16 | |||||||
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trimAl Resource Report Resource Website 500+ mentions |
trimAl (RRID:SCR_017334) | data analysis software, data processing software, software application, software resource | Software tool for automated removal of spurious sequences or poorly aligned regions from multiple sequence alignment. Software package for automated alignment trimming in large scale phylogenetic analyses. | removal, spurious, sequence, poorly, aligned, region, multiple, alignment, trimming, large, scale, phylogenetic, analysis, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
FIS ; MEC |
PMID:19505945 | Free, Available for download, Freely available | biotools:trimal | https://vicfero.github.io/trimal/, https://bio.tools/trimal | SCR_017334 | 2026-08-29 11:25:36 | 673 | ||||||
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HomoplasyFinder Resource Report Resource Website 1+ mentions |
HomoplasyFinder (RRID:SCR_017300) | data analysis software, data processing software, software application, software resource, software toolkit, standalone software | Software tool to identify and annotate homoplasies on phylogeny and sequence alignment. Used to automatically identify any homoplasies present in simulated and real phylogenetic data. Java application that can be used as standalone tool or within statistical programming environment R. | homoplasy, phylogeny, sequence, alignment, identify, data, annotate | Science Foundation Ireland | PMID:30663960 | Free, Available for download, Freely available | https://github.com/JosephCrispell/homoplasyFinder | SCR_017300 | 2026-08-29 11:25:34 | 6 | ||||||||
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BEAST2 Resource Report Resource Website 100+ mentions |
BEAST2 (RRID:SCR_017307) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software package for advanced Bayesian evolutionary analysis by sampling trees. Used for phylogenetics, population genetics and phylodynamics. Program for Bayesian phylogenetic analysis of molecular sequences. Estimates rooted, time measured phylogenies using strict or relaxed molecular clock models. Framework can be extended by third parties. Comprised of standalone programs including BEAUti, BEAST, MASTER, RBS, SNAPP, MultiTypeTree, BDSKY, LogAnalyser, LogCombiner, TreeAnnotator, DensiTree and package manager. | Bayesian, evolutionary, sampling, tree, phylogenic, analysis, Markov, chain, monte carlo, phylogenetic, population, genetic, phylodynamic, sequence |
is related to: BASTA is related to: BEAST is related to: PhyDyn has parent organization: University of Auckland; Auckland; New Zealand |
EMBL ; European Research Council ; Max Planck Society ; NIGMS U01 GM110749; Royal Society of New Zealand Marsden award ; Swiss National Science foundation |
PMID:30958812 | Free, Available for download, Freely available | SCR_017307 | , Beast 2.5 | 2026-08-29 11:25:58 | 211 |
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