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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Gubbins Resource Report Resource Website 500+ mentions |
Gubbins (RRID:SCR_016131) | software resource, software application, sequence analysis software, data analysis software, data processing software | Software application as an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. It is used for phylogenetic analysis of genome sequences and generating highly accurate reconstructions under realistic models of short-term bacterial evolution. | rapid, phylogenetic, analysis, large, sample, recombinant, bacteria, whole, genome, sequence, loci, elevated, densities, base, substitiution, mutatiion, outside, region, evolution, alignment |
is listed by: Debian is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust 098051 | PMID:25414349 | Free, Available for download | OMICS_14386 | https://sources.debian.org/src/gubbins/ | SCR_016131 | Gubbins: Genealogies Unbiased By recomBinations In Nucleotide Sequences | 2025-04-03 11:12:31 | 527 | |||||
|
Garlic Resource Report Resource Website 10+ mentions |
Garlic (RRID:SCR_016118) | software resource, software application, sequence analysis software, data analysis software, data processing software, data visualization software | Software application for visualization and editing of biomolecules. Used for the investigation of membrane proteins, visualization of other proteins and geometric objects, and analysis of protein sequences. | visualization, editing, biomolecule, investigation, membrane, protein, analyze, sequence |
is listed by: Debian is listed by: OMICtools |
Open source, Free, Available for download | OMICS_21303 | https://sources.debian.org/src/garlic/ | SCR_016118 | 2025-04-03 11:12:30 | 33 | ||||||||
|
DISULFIND Resource Report Resource Website 50+ mentions |
DISULFIND (RRID:SCR_016072) | Disulfinder | software resource, software application, sequence analysis software, data analysis software, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023, Software for predicting the disulfide bonding state of cysteines and their disulfide connectivity, starting from a protein sequence alone and may be useful in other genomic annotation tasks. | predict, disulfide, bonding, state, cysteine, protein, sequence, genomic, annotation, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools has parent organization: University of Florence; Florence; Italy |
EU STREP APrIL II contract no. FP6-508861; EU NoE BIOPATTERN contract no. FP6-508803; Embark Fellowship from the Irish Research Council for Science ; Engineering and Technology |
PMID:16844986 DOI:10.1093/nar/gkl266 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04214, biotools:disulfind | https://bio.tools/disulfind https://sources.debian.org/src/disulfinder/ |
SCR_016072 | Cysteines Disulfide Bonding State and Connectivity Predictor | 2025-04-03 11:12:25 | 66 | ||||
|
Dotter Resource Report Resource Website 50+ mentions |
Dotter (RRID:SCR_016080) | alignment software, software resource, image analysis software, software application, sequence analysis software, data analysis software, data processing software, data visualization software | Software for sequence alignment that is a graphical dot-matrix program for detailed comparison of two sequences. | sequence, alignment, graphical, dot-matrix, program, comparison, two, detail |
is related to: SEQtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust Grant 098051; NHGRI U54 HG00455 |
PMID:26801397 | Free, Available for download | SCR_016080 | Seqtools Dotter | 2025-04-03 11:12:25 | 83 | |||||||
|
Gff2aplot Resource Report Resource Website |
Gff2aplot (RRID:SCR_016128) | software resource, data processing software, software application, data visualization software | Software application to visualize the alignment of two genomic sequences together with their annotations. Used to generate print-quality images for comparative genome sequence analysis. | alignment, pair-wise, plot, genomic, sequence, visualize, together, annotate, analysis, parameter, dataset, |
is listed by: Debian is listed by: OMICtools |
PMID:14668236 | Free, Available for download | OMICS_19949 | https://sources.debian.org/src/gff2aplot/ | SCR_016128 | 2025-04-03 11:12:30 | 0 | |||||||
|
Gentle Resource Report Resource Website 1+ mentions |
Gentle (RRID:SCR_016127) | software resource, software application, software toolkit, sequence analysis software, data analysis software, data processing software | Software for DNA and amino acid editing, database management, plasmid maps, It can also be used for restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and more. | editing, database, management, plasmid maps, restriction, ligation, alignments, sequence, data, import, calculator, gel, image, display, PCR, cloning, genetic |
is listed by: Debian is listed by: OMICtools has parent organization: University of Cologne; Cologne; Germany |
Free Software Foundation | Free, Available for download | OMICS_18307 | https://sources.debian.org/src/gentle/ | SCR_016127 | GENtle | 2025-04-03 11:12:30 | 6 | ||||||
|
Exonerate Resource Report Resource Website 100+ mentions |
Exonerate (RRID:SCR_016088) | software resource, image analysis software, software application, software toolkit, alignment software, data processing software | Software package for sequence alignment of pairwise sequence comparison. Exonerate can be used to align sequences using many alignment models, exhaustive dynamic programming, or a variety of heuristics. | sequence, alignment, pairwise, comparison, dynamic, programming, heuristic, bio.tools |
is used by: ExonerateTransferAnnotation is listed by: Debian is listed by: bio.tools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:15713233 | Free, Available for download | biotools:exonerate | https://bio.tools/exonerate | SCR_016088 | 2025-04-03 11:12:26 | 345 | |||||||
|
Cassiopee Resource Report Resource Website |
Cassiopee (RRID:SCR_016056) | software resource, software application, sequence analysis software, data analysis software, data processing software | Software to scan an input genomic sequence (dna/rna/protein). It searchs for a subsequence that has an exact match, substitutions (Hamming distance), and/or insertion/deletions with supporting alphabet ambiguity. | genomic, sequence, DNA, RNA, protein, scan, subsequence, search, match, substitution, distance, Hamming, insertion, deletion |
is listed by: Debian is listed by: OMICtools has parent organization: Durham University; Durham; England |
Free, Available for download | OMICS_19794 | https://sources.debian.org/src/cassiopee/ | SCR_016056 | cassiopee-c | 2025-04-03 11:12:23 | 0 | |||||||
|
Cdbfasta Resource Report Resource Website |
Cdbfasta (RRID:SCR_016057) | CDB | software resource, software application, software toolkit, data compression software, data processing software, data transfer software | Software tool for indexing and retrieval of nucleotide sequences from FASTA (DNA and protein sequence alignment software) record databases. It has the option to compress data records. | index, retrieval, nucleotide, sequence, fasta, database, multi file, compress, record |
is listed by: Debian is listed by: OMICtools has parent organization: Carnegie Mellon University; Pennsylvania; USA has parent organization: University of Pittsburgh; Pennsylvania; USA |
The Free Software Foundation (FSF) | Free, Available for download | OMICS_19793 | https://github.com/gpertea/cdbfasta https://sources.debian.org/src/cdbfasta/ |
SCR_016057 | Constant DataBase | 2025-04-03 11:12:23 | 0 | |||||
|
Clonalframe Resource Report Resource Website 100+ mentions |
Clonalframe (RRID:SCR_016060) | software resource, software application, sequence analysis software, data analysis software, data processing software | Software package for the inference of bacterial microevolution using multilocus sequence data. It is used to identify the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance. | analysis, sequence, inference, bacteria, microevolution, multilocus, clonal, sample, chromosome, homologuous, recombination, disrupted, inheritance, DNA, genome |
is listed by: Debian is listed by: OMICtools is related to: Imperial College London; London; United Kingdom is related to: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust | DOI:10.1534/genetics.106.063305 | Free, Available for download | OMICS_14623 | https://github.com/xavierdidelot/ClonalFrameML https://sources.debian.org/src/clonalframe/ |
SCR_016060 | ClonalFrameML | 2025-04-03 11:12:23 | 125 | |||||
|
Daligner Resource Report Resource Website 10+ mentions |
Daligner (RRID:SCR_016066) | software resource, image analysis software, software application, software toolkit, alignment software, data processing software | Software alignment tool to find all significant local alignments between long and noisy, up to 15% on average reads encoded in a Dazzler database. Used for DNA sequence assembly, specifically for next generation long-read sequencers such as the Pacbio RS II and Sequel sequencers. | alignment, read, encode, dazzler, database, DNA, sequence, assembly, next, generation |
uses: Dazzler is listed by: Debian has parent organization: Max Planck Institute of Molecular Cell Biology and Genetics; Dresden; Germany |
DOI:10.1007/978-3-662-44753-6_5 | Free, Available for download | https://sources.debian.org/src/daligner/ | SCR_016066 | 2025-04-03 11:12:24 | 17 | ||||||||
|
NCBI Genome Resource Report Resource Website 500+ mentions |
NCBI Genome (RRID:SCR_002474) | Genome | data or information resource, storage service resource, service resource, database, data repository | Database that organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations in six major organism groups: Archaea, Bacteria, Eukaryotes, Viruses, Viroids, and Plasmids. Genomes of over 1,200 organisms can be found in this database, representing both completely sequenced organisms and those for which sequencing is in progress. Users can browse by organism, and view genome maps and protein clusters. Links to other prokaryotic and archaeal genome projects, as well as BLAST tools and access to the rest of the NCBI online resources are available. | chromosome, organelle, plasmid, viroid, virus, genome, sequence, map, assembly, annotation, gene mapping, dna, blast, protein cluster, gold standard |
is listed by: re3data.org is related to: MapViewer is related to: UniProt Proteomes is related to: CaspBase has parent organization: NCBI |
Free, Freely avaialble | nif-0000-02802 | http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Genome | SCR_002474 | Entrez Genomes, Entrez Genome, NCBI, Genome, Genome Database, Genome: Information by genome sequence | 2025-04-03 11:01:38 | 523 | ||||||
|
Sal-Site Resource Report Resource Website 50+ mentions |
Sal-Site (RRID:SCR_002850) | Sal-Site | organism-related portal, data or information resource, image collection, analysis service resource, portal, service resource, production service resource, database, topical portal, data analysis service | Portal that supports Ambystoma-related research and educational efforts. It is composed of several resources: Salamander Genome Project, Ambystoma EST Database, Ambystoma Gene Collection, Ambystoma Map and Marker Collection, Ambystoma Genetic Stock Center, and Ambystoma Research Coordination Network. | gene, genomic, expressed sequence tag, blast, model organism, genome, salamander, animal model, genetic map, genetic marker, gene expression, limb regeneration, microarray, quantitative-pcr, rna-seq, nanostring, husbandry, embryo, limb, mutant, strain, neural, olfaction, phentotype, regeneration, renal, retina, sequence, vision, human, chicken, xenopus tropicalis, FASEB list | has parent organization: University of Kentucky; Kentucky; USA | NSF OB0242833; NSF DBI0443496; NCRR R24 RR016344; NIH Office of the Director R24 OD010435 |
PMID:16359543 | nif-0000-25309 | https://orip.nih.gov/comparative-medicine/programs/vertebrate-models | SCR_002850 | Ambystoma Resources for Model Amphibians Database | 2025-04-03 11:02:12 | 92 | |||||
|
Rainbow Resource Report Resource Website 10+ mentions |
Rainbow (RRID:SCR_002724) | software resource, software application, sequence analysis software, data analysis software, data processing software | Software developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. | software, tool, clustering, assembling, short, read, restriction, site, DNA, sequence, analysis, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:22942077 DOI:10.1093/bioinformatics/bts482 |
Free, Freely available, Available for download | SCR_015992, OMICS_03722, biotools:rainbow | https://bio.tools/rainbow https://sources.debian.org/src/bio-rainbow/ |
SCR_002724 | RAD-seq: Restriction-site Associated DNA sequencing, Bio-rainbow, RAD-seq | 2025-04-03 11:02:01 | 37 | ||||||
|
Gabi Primary Database Resource Report Resource Website 10+ mentions |
Gabi Primary Database (RRID:SCR_002755) | GABI | data or information resource, data analysis service, storage service resource, analysis service resource, service resource, production service resource, database, data repository |
Database that collects, integrates and links all relevant primary information from the GABI plant genome research projects and makes them accessible via internet. Its purpose is to support plant genome research in Germany, to yield information about commercial important plant genomes, and to establish a scientific network within plant genomic research. GreenCards is the main interface for text based retrieval of sequence, SNP, mapping data etc. Sharing and interchange of data among collaborating research groups, industry and the patent- and licensing agency are facilitated. * GreenCards: Text based search for sequence, mapping, SNP data etc. * Maps: Visualization of genetic or physical maps. * BLAST: Secure BLAST search against different public databases or non-public sequence data stored in GabiPD. * Proteomics: View interactive 2D-gels and view or download information for identified protein spots. Registered users can submit data via secure file upload. |
molecular plant physiology, plant genome, genome, blast, sequence, snp, mapping, proteomics, image collection | has parent organization: Max Planck Institute of Molecular Plant Physiology; Golm; Germany | German Resource Center for Genome Research RZPD GmbH ; Max Planck Society ; BMBF 0312272; BMBF 0313112; BMBF 0315046 |
PMID:18812395 | nif-0000-02866 | http://gabi.rzpd.de/ | SCR_002755 | GabiPD | 2025-04-03 11:02:04 | 13 | |||||
|
DnaSP Resource Report Resource Website 5000+ mentions |
DnaSP (RRID:SCR_003067) | DnaSP | data analysis software, software resource, data processing software, software application | A software package for the analysis of nucleotide polymorphism from aligned DNA sequence data. DnaSP can estimate several measures of DNA sequence variation within and between populations (in noncoding, synonymous or nonsynonymous sites, or in various sorts of codon positions), as well as linkage disequilibrium, recombination, gene flow and gene conversion parameters. DnaSP can also carry out several tests of neutrality: Hudson, Kreitman and Aguad (1987), Tajima (1989), McDonald and Kreitman (1991), Fu and Li (1993), and Fu (1997) tests. Additionally, DnaSP can estimate the confidence intervals of some test-statistics by the coalescent. The results of the analyses are displayed on tabular and graphic form. | genetics, dna, population genetics, sequence, polymorphism, nucleotide polymorphism, dna sequence, population, noncoding, synonymous, nonsynonymous |
is listed by: OMICtools has parent organization: University of Barcelona; Barcelona; Spain |
Spanish Direccion General de Investigacion Cientifica y Technica PB91-0245; Spanish Direccion General de Investigacion Cientifica y Technica PB94-0923; Spanish Direccion General de Investigacion Cientifica y Technica PB97-0918; Spanish Direccion General de Investigacion Cientifica y Technica TXT98-1802; Spanish Direccion General de Investigacion Cientifica y Technica BMC2001-2906; Spanish Direccion General de Investigacion Cientifica y Technica BFU2004-02253; Spanish Direccion General de Investigacion Cientifica y Technica BFU2007-6292 |
PMID:19346325 PMID:19378153 PMID:14668244 PMID:10089204 PMID:9183537 PMID:8808578 |
Free for academic use | OMICS_01820, nif-0000-30461 | SCR_003067 | DNA Sequence Polymorphism | 2025-04-03 11:02:35 | 5569 | |||||
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GenePaint Resource Report Resource Website 100+ mentions |
GenePaint (RRID:SCR_003015) | GenePaint.org | data or information resource, reference atlas, atlas, database, expression atlas | Digital atlas of gene expression patterns in developing and adult mouse. Several reference atlases are also available through this site. Expression patterns are determined by non-radioactive in situ hybridization on serial tissue sections. Sections are available from several developmental ages: E10.5, E14.5 (whole embryos), E15.5, P7 and P56 (brains only). To retrieve expression patterns, search by gene name, site of expression, GenBank accession number or sequence homology. For viewing expression patterns, GenePaint.org features virtual microscope tool that enables zooming into images down to cellular resolution. | gene expression, adult mouse, annotated, c57bl6, mouse, mouse embryo, mrna, non radioactive in situ hybridization, light microscopy, molecular neuroanatomy resource, in situ hybridization, embryonic, postnatal, adult, brain, head, annotation, rna probe, sequence, anatomical structure, FASEB list |
has parent organization: Max Planck Institute for Biophysical Chemistry; Gottingen; Germany is parent organization of: GenePaint E15 Atlas is parent organization of: GenePaint P7 Atlas is parent organization of: GenePaint P56 Mouse Atlas is parent organization of: GenePaint Interactive Anatomy Atlas |
Burroughs Wellcome Fund ; European Union ; Max Planck Society ; Merck Genome Research Institute ; Romansky Endowment ; NINDS ; BMBF |
PMID:14681479 PMID:22936000 |
nif-0000-00009, SCR_017526 | SCR_003015 | Atlas of Gene Expression Patterns in Mouse Embryo | 2025-04-03 11:02:29 | 160 | ||||||
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Computational Biology Center Resource Report Resource Website 10+ mentions |
Computational Biology Center (RRID:SCR_002877) | data or information resource, training resource, portal, topical portal, disease-related portal | Computational biology research at Memorial Sloan-Kettering Cancer Center (MSKCC) pursues computational biology research projects and the development of bioinformatics resources in the areas of: sequence-structure analysis; gene regulation; molecular pathways and networks, and diagnostic and prognostic indicators. The mission of cBio is to move the theoretical methods and genome-scale data resources of computational biology into everyday laboratory practice and use, and is reflected in the organization of cBio into research and service components ~ the intention being that new computational methods created through the process of scientific inquiry should be generalized and supported as open-source and shared community resources. Faculty from cBio participate in graduate training provided through the following graduate programs: * Gerstner Sloan-Kettering Graduate School of Biomedical Sciences * Graduate Training Program in Computational Biology and Medicine Integral to much of the research and service work performed by cBio is the creation and use of software tools and data resources. The tools that we have created and utilize provide evidence of our involvement in the following areas: * Cancer Genomics * Data Repositories * iPhone & iPod Touch * microRNAs * Pathways * Protein Function * Text Analysis * Transcription Profiling | drug, evolution, experiment, gene, algorithm, bioinformatics, biology, cancer, clinical, computational, diagnostic, genome, human, initiation, kinetics, laboratory, leukemia, ligand, metastasis, microrna, mirna, model, molecular, network, pathway, phenotype, prognostic, progression, protein, regulation, research, resistance, rna, sequence, stem cell, structure, t cell, therapy, treatment, tumor | is parent organization of: TMBETA-GENOME- Annotation of Beta-Barrel Membrane Proteins in Genomic Sequences | nif-0000-25560 | SCR_002877 | cBio | 2025-04-03 11:02:15 | 13 | |||||||||
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DIALIGN Resource Report Resource Website 10+ mentions |
DIALIGN (RRID:SCR_003041) | DIALIGN | software resource, data access protocol, web service, analysis service resource, service resource, production service resource, data analysis service | Tool for multiple sequence alignment using various sources of external information that is particularly useful to detect local homologies in sequences with low overall similarity. While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing entire segments of the sequences. No gap penalty is used. This approach can be used for both global and local alignment, but it is particularly successful in situations where sequences share only local homologies. Several versions of DIALIGN are available online at GOBICS, http://dialign.gobics.de/ | dna, protein, sequence alignment, sequence, alignment, fasta, genome, genomic sequence, homology, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Bielefeld University; North Rhine-Westphalia; Germany |
PMID:15215344 PMID:23620293 DOI:10.1186/1748-7188-3-6 |
Acknowledgement requested | nif-0000-30417, OMICS_24606, OMICS_00973, biotools:dialign-tx | http://dialign.gobics.de/ https://bio.tools/dialign-tx |
https://sources.debian.org/src/dialign-tx/ | SCR_003041 | DIALIGN at GOBICS | 2025-04-03 11:02:32 | 41 | ||||
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Tuschl Laboratory: RNA Molecular Biology Resource Report Resource Website 1+ mentions |
Tuschl Laboratory: RNA Molecular Biology (RRID:SCR_002866) | portal, organization portal, data or information resource, laboratory portal | RNA is not only a carrier of genetic information, but also a catalyst and a guide for sequence-specific recognition and processing of other RNA molecules. This lab investigates the regulatory mechanisms of RNA interference, RNA-mediated translational control, and nuclear pre-mRNA splicing. Classical and combinatorial biochemical techniques are used to analyze the function of the RNA- and protein-components involved in those processes. | genetics, biochemical, biology, catalyst, mechanism, mirna, molecule, process., protein, regulation, rna, sequence, sirna, technique | has parent organization: Rockefeller University; New York; USA | nif-0000-25546 | http://www.rockefeller.edu/labheads/tuschl/sirna.html | SCR_002866 | Tuschl Lbaoratory | 2025-04-03 11:02:14 | 5 |
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