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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Joint Center for Structural Genomics Resource Report Resource Website 50+ mentions |
Joint Center for Structural Genomics (RRID:SCR_008251) | JCSG | institution | The JCSG is a multi-institutional consortium that aims to explore the expanding protein universe to find new challenges and opportunities to significantly contribute to new biology, chemistry and medicine through development of HT approaches to structural genomics. The mission of JCSG is to to operate a robust HT protein structure determination pipeline as a large-scale production center for PSI-2. A major goal is to ensure that innovative high-throughput approaches are developed that advance not only structural genomics, but also structural biology in general, via investigation of large numbers of high-value structures that populate protein fold and family space and by increasing the efficiency of structure determination at substantially reduced cost. The JCSG centralizes each core activity into single dedicated sites, each handling distinct, but interconnected objectives. This unique approach allows each specialized group to focus on its own area of expertise and provides well-defined interfaces among the groups. In addition, this approach addresses the requirements for the scalability needed to process large numbers of targets at a greatly reduced cost per target. JCSG production groups are: - Administrative Core - Bioinformatics Core - Crystallomics Core - Structure Determination Core - NMR Core JCSG is deeply committed to the development of new technologies that facilitate high throughput structural genomics. The areas of development include hardware, software, new experimental methods, and adaptation of existing technologies to advance genome research. In the hardware arena, their commitment is to the development of technologies that accelerate structure solution by increasing throughput rates at every stage of the production pipeline. Therefore, one major area of hardware development has been the implementation of robotics. In the software arena, they have developed enterprise resource software that track success, failures, and sample histories from target selection to PDB deposition, annotation and target management tools, and helper applications aimed at facilitating and automating multiple steps in the pipeline. Sponsors: The Joint Center for Structural Genomics is funded by the National Institute of General Medical Sciences (NIGMS), as part of the second phase of the Protein Structure Initiative (PSI) of the National Institutes of Health (U54 GM074898). | exclusion chromatography, expression, fine-structure spectroscopy, fold, absorption, affinity, bacterial, baculovirus, bioinformatics, biology, biophysical, cell, chemistry, cloning, crystallization, crystallomics, differential scanning calorimetry, diffraction, domain, genomic, gnfuge, growth, hardware, ief gel electrophoresis, macromoleuclar, medicine, microexpression, mouse, nmr, optical density, physicochemical, protein, purification, recombinatorial, robotics, sds-page, sequence, software, structural, structural biology, structure, technology, thermocycler, topoisomerase, tryptic mass spectrometry, uv/vis absorbance scan, x-ray |
has parent organization: University of California at San Diego; California; USA has parent organization: Scripps Research Institute has parent organization: Sanford Burnham Prebys Medical Discovery Institute has parent organization: Stanford University; Stanford; California |
nif-0000-22295, grid.419677.a | https://ror.org/00exr1241 | SCR_008251 | JCSG | 2026-08-29 11:23:28 | 99 | |||||||
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Protein Databank Fun Resource Report Resource Website 1+ mentions |
Protein Databank Fun (RRID:SCR_008226) | data analysis software, data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. PDBfun is a web server for structural and functional analysis of proteins at the residue level. pdbFun gives fast access to the whole Protein Data Bank (PDB) organized as a database of annotated residues. The available data (features) range from solvent exposure to ligand binding ability, location in a protein cavity, secondary structure, residue type, sequence functional pattern, protein domain and catalytic activity. PDBfun is an integrated web tool for querying the PDB at the residue level and for local structural comparison. It integrates knowledge on single residues in protein structures coming from other databases or calculated with available or in-house developed instruments for structural analysis. Each set of different annotations represents a feature. Features are listed in PDBfun main page in orange. Features can be used for building residues selections. | functional, 2d, ability, activity, analysis, binding, catalytic, cavity, chain, cleft, domain, ligand, location, motif, protein, protein structure databases, residue, secondary, sequence, size, solvent, structural, structure, surface | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21315 | SCR_008226 | PDBfun | 2026-08-29 11:23:10 | 2 | |||||||||
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Affymetrix Power Tools Resource Report Resource Website 10+ mentions |
Affymetrix Power Tools (RRID:SCR_008401) | software resource | Affymetrix Power Tools (APT) are a set of cross-platform command line programs that implement algorithms for analyzing and working with Affymetrix GeneChip arrays. APT programs are intended for power users who prefer programs that can be utilized in scripting environments and are sophisticated enough to handle the complexity of extra features and functionality. APT provides platform for developing and deploying new algorithms without waiting for the GUI implementations. This resource is supported by Affymetrix, Inc. | Affymetrix, Inc., Genomics, Clinical, Study, Bioinformatic, Windows, MacOS, Linux, resource, Data, Normalization, Sequence, Annotation, Gene, Expression, Pattern, Motif, Inference, Toolkit, Model, Fitting, Algorithm |
has parent organization: Affymetrix has parent organization: Affymetrix |
nif-0000-30070 | https://www.affymetrix.com/support/developer/powertools/changelog/install.html, https://media.affymetrix.com/support/developer/powertools/changelog/index.html | http://www.affymetrix.com/partners_programs/programs/developer/tools/powertools.affx | SCR_008401 | APT | 2026-08-29 11:23:04 | 32 | |||||||
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ProP Server Resource Report Resource Website 50+ mentions |
ProP Server (RRID:SCR_014936) | software resource, web application | 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 | 2026-08-29 11:28:17 | 78 | ||||||
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CD-HIT-OTU Resource Report Resource Website 50+ mentions |
CD-HIT-OTU (RRID:SCR_006983) | CD-HIT-OTU | software resource | Data analysis service and software program that perform Operantional Taxonomic Units (OTUs) finding. It uses a three-step clustering for identifying OTUs. The first-step clustering is raw read filtering and trimming. The second step is error-free reads picking.. At the last step, OTU clustering is done at different distanct cutoffs (0.01, 0.02, 0.03... 0.12). | 454, read, illumina, rrna, fasta, metagenome, sequence, clustering, metagenomics, next-generation sequencing, protein |
is listed by: OMICtools has parent organization: CD-HIT |
PMID:22772836 PMID:21899761 |
GNU General Public License, v2, Acknowledgement requested | OMICS_01441 | SCR_006983 | 2026-08-29 11:22:49 | 89 | |||||||
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GOblet Resource Report Resource Website 1+ mentions |
GOblet (RRID:SCR_006998) | GOblet | analysis service resource, data analysis service, production service resource, service resource, software application, software resource | Tool that performs annotation based on GO and pathway terms for anonymous cDNA or protein sequences. It uses the species independent GO structure and vocabulary together with a series of protein databases collected from various sites, to perform a detailed GO annotation by sequence similarity searches. The sensitivity and the reference protein sets can be selected by the user. GOblet runs automatically and is available as a public service on our web server. GOblet expects query sequences to be in FASTA-Format (with header-lines). Protein and nucleotide sequences are accepted. Total size of all sequences submitted per request should not be larger than 50kb currently. For security reasons: Larger post's will be rejected. Due to limited capacities the queries may be processed in batches depending on the server load. The output of the BLAST job is filtered automatically and the relevant hits are displayed. In addition, the respective GO-terms are shown together with the complete GO-hierarchy of parent terms., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, sequence, cdna, ontology or annotation browser, pathway, term enrichment, clustering, virus, genomic, protein, nucleotide |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology has parent organization: Max Planck Institute for Molecular Genetics; Berlin; Germany |
BMBF | PMID:20134064 PMID:15215401 PMID:12824400 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30624, OMICS_02271 | http://goblet.molgen.mpg.de | SCR_006998 | 2026-08-29 11:22:58 | 6 | |||||
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NAST Resource Report Resource Website 50+ mentions |
NAST (RRID:SCR_006995) | NAST | simulation software, software application, software resource | A knowledge-based coarse-grained tool for modeling RNA structures. It produces a diverse set of plausible 3D structures that satisfy user-provided constraints based on: 1. primary sequence 2. known or predicted secondary structure 3. known or predicted tertiary contacts (optional) Additionally, NAST can use residue-resolution experimental data (e.g. hydroxyl radical footprinting) to filter the generated decoy structures. NAST uses an RNA-specific knowledge-based potential in a coarse-grained molecular dynamics engine to generate large numbers of plausible 3D structures that satisfy the constraints given on the secondary and tertiary structure. It then filter these structures based on agreement to the experimental data (if available). This results in a model of the molecule which satisfies all the known residue-resolution data. Imported from BiositeMaps registry | 3d, nucleic acid, primary, rna, secondary, sequence, simulation, structure, tertiary, tool | nif-0000-23333 | SCR_006995 | The Nucleic Acid Simulation Tool (NAST), The Nucleic Acid Simulation Tool | 2026-08-29 11:22:58 | 68 | |||||||||
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YeTFaSCo Resource Report Resource Website 10+ mentions |
YeTFaSCo (RRID:SCR_006893) | YeTFaSCo | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | Collection of all available transcription factor (TF) specificities for the yeast Saccharomyces cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats. The specificities are evaluated for quality using several metrics. With this website, you can scan sequences with the motifs to find where potential binding sites lie, inspect precomputed genome-wide binding sites, find which TFs have similar motifs to one you have found, and download the collection of motifs. Submissions are welcome. | transcription factor, binding site, sequence, yeast, motif, gene, genome, protein, protein complex |
is listed by: OMICtools is related to: Gene Ontology has parent organization: University of Toronto; Ontario; Canada |
Ontario Graduate Scholarship awards ; Canadian Institutes of Health Research Operating Grant MOP-490425; Canadian Institutes of Health Research Operating Grant MOP-86705 |
PMID:22102575 | Acknowledgement requested | nlx_151611, OMICS_01861 | SCR_006893 | Yeast Transcription Factor Specificity Compendium, YeTFaSCo: The Yeast Transcription Factor Specificity Compendium | 2026-08-29 11:22:55 | 34 | |||||
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HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism Resource Report Resource Website 50+ mentions |
HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism (RRID:SCR_007050) | HumanCyc | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource, software resource | The HumanCyc database describes human metabolic pathways and the human genome. By presenting metabolic pathways as an organizing framework for the human genome, HumanCyc provides the user with an extended dimension for functional analysis of Homo sapiens at the genomic level. A computational pathway analysis of the human genome assigned human enzymes to predicted metabolic pathways. Pathway assignments place genes in their larger biological context, and are a necessary step toward quantitative modeling of metabolism. HumanCyc contains the complete genome sequence of Homo sapiens, as presented in Build 31. Data on the human genome from Ensembl, LocusLink and GenBank were carefully merged to create a minimally redundant human gene set to serve as an input to SRI''s PathoLogic software, which generated the database and predicted Homo sapiens metabolic pathways from functional information contained in the genome''s annotation. SRI did not re-annotate the genome, but worked with the gene function assignments in Ensembl, LocusLink, and GenBank. The resulting pathway/genome database (PGDB) includes information on 28,783 genes, their products and the metabolic reactions and pathways they catalyze. Also included are many links to other databases and publications. The Pathway Tools software/database bundle includes HumanCyc and the Pathway Tools software suite and is available under license. This form of HumanCyc is faster and more powerful than the Web version. | enzyme, function, functional, gene, genome, genomic, human, human genome, metabolic, metabolism, mitochondrion, nucleotide, pathway, position, reaction, sequence, metabolomics, gene expression, bioreaction, metabolic pathway, nutrition, FASEB list |
is listed by: BioCyc is related to: Pathway Commons is related to: ConsensusPathDB is related to: BioCyc is related to: Pathway Tools has parent organization: Stanford Research Institute International |
Pharmaceutical company ; NIGMS GM092729 |
PMID:15642094 | Public | r3d100011286, nif-0000-21206 | https://doi.org/10.17616/R3ZS72 | SCR_007050 | 2026-08-29 11:22:46 | 65 | |||||
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Malaria Parasite Metabolic Pathways Resource Report Resource Website 10+ mentions |
Malaria Parasite Metabolic Pathways (RRID:SCR_007072) | Malaria Parasite Metabolic Pathways | data or information resource, data set, image collection | Data set of metabolic pathways for the malaria parasite based on the present knowledge of parasite biochemistry and on pathways known to occur in other unicellular eukaryotes. This site extracted the pertinent information from the universal sites and presented them in an educative and informative format. The site also includes, cell-cell interactions (cytoadherence and rosetting), invasion of the erythrocyte by the parasite and transport functions. It also contains an artistic impression of the ultrastructural morphology of the interaerythrocytic cycle stages and some details about the morphology of mitochondria and the apicoplast. Most pathways are relevant to the erythrocytic phase of the parasite cycle. All maps were checked for the presence of enzyme-coding genes as they are officially annotated in the Plasmodium genome (http://plasmodb.org/). The site is constructed in a hierarchical pattern that permits logical deepening: * Grouped pathways of major chemical components or biological process ** Specific pathways or specific process *** Chemical structures of substrates and products or process **** Names of enzymes and their genes or components of process Each map is linked to other maps thus enabling to verify the origin of a substrate or the fate of a product. Clicking on the EC number that appears next to each enzyme, connects the site to BRENDA, SWISSPROT ExPASy ENZYME, PlasmoDB and to IUBMB reaction scheme. Clicking of the name of a metabolite, connects the site to KEGG thus providing its chemical structure and formula. Next to each enzyme there is a pie that depicts the stage-dependent transcription of the enzyme''s coding gene. The pie is constructed as a clock of the 48 hours of the parasite cycle, where red signifies over-transcription and green, under-transcription. Clicking on the pie links to the DeRisi/UCSF transcriptome database. | enzyme, gene, genome, map, metabolic, mosquito, parasite, pathway, plasmodium falciparum, protein, reaction, sequence, metabolic pathway, chemical structure, cell-cell interaction, transport, morphology, mitochondria, apicoplast | has parent organization: Hebrew University of Jerusalem; Jerusalem; Israel | Malaria | UNDP/World Bank/WHO Special Programme ; NIAID ; European Union ; 6th FP- BioMalPar Network of Excellence on Biology and Pathology of the Malaria Parasite |
nif-0000-21249 | SCR_007072 | 2026-08-29 11:23:00 | 20 | |||||||
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BioInfoBank Meta Server Resource Report Resource Website 10+ mentions |
BioInfoBank Meta Server (RRID:SCR_007181) | BioInfoBank | data or information resource, portal, topical portal | This service offers a gateway to well-benchmarked protein structure and function prediction methods. Structural models collected from the prediction servers are assessed using the powerful 3D-jury consensus approach. The Structure Prediction Meta Server provides access to various fold recognition, function prediction and local structure prediction methods. The Server takes the amino acid sequence of the query protein, the reference name for the prediction job, and the E-mail address as input. The E-mail address is used only for notification about errors during the execution of the job. The query sequence and the reference name are placed in the process queue. The Meta Server accepts only sequences, which have not been submitted before. In case of duplicate sequences the second user will be notified with a link to the previous submission. Sequences longer than 800 amino acids are not accepted by some services. The internal SQL database offers the possibility to find any previous jobs processed by the Meta Server using regular expressions addressing field like E-mail, Job Name and the host name, from which the job was initiated. Each server has its own process queuing system managed by the Meta Server. All results of fold recognition servers are translated into uniform formats. The information extracted from the raw output of the servers includes the PDB codes of the hits, the alignments and the similarity (reliability) scores specific for every server. Mapping of the hits to the SCOP and FSSP classifications are made either using known PDB representatives or alignment of the template sequence with the databases of proteins in both classifications. The secondary structure assignments for all hits are taken from the mapped FSSP (red for helices and blue for strands). Underscored amino acids indicate the first residue after an insertion in the template sequence. The Meta server provides translation of the alignments in standard formats like FASTA, PDB or CASP. The Meta Server is coupled to consensus servers. They provide jury predictions based on the results collected from other services. Not all fold recognition servers are used by the jury system. The data stored on the meta server is available through http://meta.bioinfo.pl/data/JOBID/. Jobs older than 2 months are not shown. The Meta Server is only a set of programs aimed to process and manage biological data, while the predictive power of the service comes from (mostly) remote prediction providers. Sponsors: This resource is supported by The BioInfoBank Institute. | server, meta, biology, function, protein, structure, method, model, prediction, 3-dimentional, amino acid, sequence | nif-0000-30180 | http://meta.bioinfo.pl | SCR_007181 | The BioInfoBank Meta Server, BioInfoBank Meta Server | 2026-08-29 11:22:52 | 22 | ||||||||
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VBASE2 Resource Report Resource Website 50+ mentions |
VBASE2 (RRID:SCR_007082) | VBASE2 | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse. It presents V gene sequences extracted from the EMBL nucleotide sequence database and Ensembl together with links to the respective source sequences. Based on the properties of the source sequences, V genes are classified into 3 different classes: * Class 1: genomic and rearranged evidence * Class 2: genomic evidence only * Class 3: rearranged evidence only This allows careful sequence quality validation by the user. References to other immunological databases ( KABAT, IMGT/LIGM and VBASE ) are given to provide all public annotation data for each V gene. The VBASE2 database can be accessed either by the Direct Query interface or by the DNAPLOT Query interface. The Sequences given by the user are aligned with DNAPLOT against the VBASE2 database. Direct Query allows to enter sequence IDs and names (Field 1), choose species, locus, V gene family and class (Field 2) or search for 100% sequences (Field 3). At the DNAPLOT Query, the sequences given by the user are aligned with DNAPLOT against the VBASE2 database. The DNAPLOT program offers V gene nucleotide sequence alignment referring to the IMGT V gene unique numbering. The Quick Search can be used either for Direct Query to search for sequence IDs and V gene names or for DNAPLOT Query for up to 5 sequences. The new Fab Analysis allows you to align Fab, scFab, scAb or scFv sequences with DNAPLOT against the VBASE2 database, where both heavy and light chain are analyzed. | v gene sequence, v gene, gene, dna, sequence, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is related to: European Nucleotide Archive (ENA) is related to: Ensembl |
BMBF 031U110A/031U210A | PMID:15608286 | Acknowledgement requested | nlx_25238, biotools:germ-line_v_genes | https://bio.tools/germ-line_v_genes | SCR_007082 | VBASE2: the integrative germ-line V gene database | 2026-08-29 11:22:50 | 74 | ||||
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BioEdit Resource Report Resource Website 10000+ mentions |
BioEdit (RRID:SCR_007361) | alignment software, data analysis software, data processing software, image analysis software, sequence analysis software, software application, software resource | Software tool as biological sequence alignment editor written for Windows 95/98/NT/2000/XP/7 and sequence analysis program. Provides sequence manipulation and analysis options and links to external analysis programs to view and manipulate sequences with simple point and click operations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | sequence, alignment, editor, analysis, program | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156845 | SCR_007361 | 2026-08-29 11:22:56 | 13403 | |||||||||
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EMBL-EBI COVID-19 Portal Resource Report Resource Website 10+ mentions |
EMBL-EBI COVID-19 Portal (RRID:SCR_018337) | data or information resource, data repository, database, disease-related portal, portal, service resource, storage service resource, topical portal | EMBL-EBI portal to enable researchers to upload, access and analyse COVID-19 related reference data and specialist datasets submitted to EMBL-EBI and other major centers for biomedical data. Used to facilitate data sharing and analysis to accelerate coronavirus research. The aim of the COVID-19 Data Portal is to facilitate data sharing and analysis, and to accelerate coronavirus research. EMBL-EBI and partners have set up the COVID-19 Data Portal, which will bring together relevant datasets submitted to EMBL-EBI and other major centres for biomedical data. The aim is to facilitate data sharing and analysis, and to accelerate coronavirus research. The COVID-19 Data Portal will enable researchers to upload, access and analyse COVID-19 related reference data and specialist datasets. The COVID-19 Data Portal will be the primary entry point into the functions of a wider project, the European COVID-19 Data Platform. | COVID-19, COVID-19 data, sequence, expression, protein sequence, protein structure, proteome, translatome, analysis, EMBL-EBI | is related to: EMBL-EBI Pathogens - COVID-19 | COVID-19 | Free, Freely available | SCR_018816 | https://www.covid19dataportal.org/, https://www.ebi.ac.uk/about/news/press-releases/embl-ebi-launches-covid-19-data-portal | SCR_018337 | EMBL-EBI COVID-19 Data Portal, COVID-19 Data Portal | 2026-08-29 11:26:06 | 20 | ||||||
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2019 Novel Coronavirus Resource (2019nCoVR) by China National Center for Bioinformation Resource Report Resource Website 1+ mentions |
2019 Novel Coronavirus Resource (2019nCoVR) by China National Center for Bioinformation (RRID:SCR_018342) | 2019nCoVR | data or information resource, disease-related portal, portal, topical portal | Bioinformation related to COVID-19. Site developed and maintained by China National Center for Bioinformation. Collection of sequences, genome variations, publication, clinical resource data. | COVID-19, sequence, genome sequence, genome variation, data, China National Center for Bioinformation | COVID-19 | Free, Freely available | SCR_018342 | 2019 Novel Coronavirus Resource, 2019 Novel Coronavirus Resource (2019nCoVR), CNCB 2019nCoVR, CNCB 2019 Novel Coronavirus Resource | 2026-08-29 11:26:06 | 4 | ||||||||
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Vmatch Resource Report Resource Website 50+ mentions |
Vmatch (RRID:SCR_018968) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for efficiently solving large scale sequence matching tasks. | Sequence analysis, large scale, sequence matching, sequence, matching, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite has parent organization: University of Hamburg; Hamburg; Germany |
Free, Available for download, Freely available | OMICS_19963, biotools:vmatch | https://bio.tools/vmatch, https://sources.debian.org/src/vmatch/ | SCR_018968 | 2026-08-29 11:26:16 | 56 | ||||||||
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GeMoMa Resource Report Resource Website 100+ mentions |
GeMoMa (RRID:SCR_017646) | simulation software, software application, software resource | Software tool as homology based gene prediction program that predicts gene models in target species based on gene models in evolutionary related reference species. Utilizes amino acid sequence conservation, intron position conservation, and RNA-seq data to accurately predict protein-coding transcripts. Supports combination of predictions based on several reference species allowing to transfer high quality annotation of different reference species to target species. | Homology, based, gene, prediction, model, target, evolutionary, related, reference, species, sequence, conservation, intron, position, RNAseq, data, protein, coding, transcript, bio.tools |
is listed by: bio.tools is listed by: Debian works with: GUSHR |
PMID:31020559 | Free, Available for download, Freely available | biotools:gemoma | https://bio.tools/gemoma | SCR_017646 | Gene Model Mapper | 2026-08-29 11:27:42 | 158 | ||||||
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StringTie Resource Report Resource Website 1000+ mentions |
StringTie (RRID:SCR_016323) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software application for assembling of RNA-Seq alignments into potential transcripts. It enables improved reconstruction of a transcriptome from RNA-seq reads. This transcript assembling and quantification program is implemented in C++ . | assembling, RNA, sequence, transcript, gene, alignment, reconstruction, read, analysis, process, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
NCI R01 CA120185; NCI R01 CA134292; NHGRI R01 HG006102; NHGRI R01 HG006677; NIGMS R01 GM105705; the Cancer Prevention and Research Institute of Texas |
PMID:25690850 DOI:10.1038/nbt.3122 |
Open source, Free, Freely available, Available for download | biotools:stringtie, OMICS_07226 | https://github.com/gpertea/stringtie, https://bio.tools/stringtie, https://sources.debian.org/src/stringtie/ | SCR_016323 | 2026-08-29 11:27:40 | 4976 | ||||||
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PseudoFuN Resource Report Resource Website 1+ mentions |
PseudoFuN (RRID:SCR_017095) | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Software as database and query tool for homologous pseudogene and coding gene families. Collection of human pseudogenes and gene associations. Supports search, graphical visualization and functional analysis of pseudogenes and coding genes based on PGG families. | gene, pseudogene, sequence, homology, regulatory, network, miRNA, coexpression, noncoding, RNA, TCGA, cancer |
has parent organization: Ohio State University; Ohio; USA has parent organization: Indiana University School of Medicine; Indiana; USA |
NLM T15 LM011270 | Free, Freely available | https://github.com/yanzhanglab/PseudoFuN_app | SCR_017095 | Pseudogene Functional Networks | 2026-08-29 11:27:42 | 2 | |||||||
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Hinge Resource Report Resource Website 1+ mentions |
Hinge (RRID:SCR_016135) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software application for long read genome assembly based on hinging. Used in long-read sequencing technologies in genome assemblies to achieve optimal repeat resolution. | long, read, genome, assembly, hinging, sequence, optimal, repeat, resolution |
is listed by: Debian is listed by: OMICtools |
PMID:28320918 | Free, Available for download | OMICS_12339 | https://sources.debian.org/src/hinge/ | SCR_016135 | 2026-08-29 11:28:07 | 9 |
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