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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PlantNATsDB - Plant Natural Antisense Transcripts DataBase Resource Report Resource Website 1+ mentions |
PlantNATsDB - Plant Natural Antisense Transcripts DataBase (RRID:SCR_013278) | PlantNATsDB | analysis service resource, production service resource, database, data analysis service, service resource, data or information resource | Natural Antisense Transcripts (NATs), a kind of regulatory RNAs, occur prevalently in plant genomes and play significant roles in physiological and/or pathological processes. PlantNATsDB (Plant Natural Antisense Transcripts DataBase) is a platform for annotating and discovering NATs by integrating various data sources involving approximately 2 million NAT pairs in 69 plant species. PlantNATsDB also provides an integrative, interactive and information-rich web graphical interface to display multidimensional data, and facilitate plant research community and the discovery of functional NATs. GO annotation and high-throughput small RNA sequencing data currently available were integrated to investigate the biological function of NATs. A ''''Gene Set Analysis'''' module based on GO annotation was designed to dig out the statistical significantly overrepresented GO categories from the specific NAT network. PlantNATsDB is currently the most comprehensive resource of NATs in the plant kingdom, which can serve as a reference database to investigate the regulatory function of NATs. | natural antisense transcript, annotation, high-throughput, small rna sequencing, function, regulatory function, predict, sequence, small rna, blast, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Gene Ontology is related to: Gene Expression Omnibus has parent organization: Zhejiang University; Zhejiang; China |
National Natural Sciences Foundation of China 30971743; National Natural Sciences Foundation of China 31050110121; National Natural Sciences Foundation of China 31071659; Ministry of Science and Technology of China 2009DFA32030; Program for New Century Excellent Talents in University of China NCET-07-0740; Huazhong Agricultural University Scientific and Technological Self-innovation Foundation 2010SC07 |
PMID:22058132 | Free | nlx_151492, biotools:plantnatsdb | https://bio.tools/plantnatsdb | SCR_013278 | Plant Natural Antisense Transcripts DataBase | 2025-04-02 11:09:53 | 9 | ||||
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Unifrac Resource Report Resource Website 500+ mentions |
Unifrac (RRID:SCR_014616) | software application, data processing software, data analysis software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented Setember 8, 2016. A suite of tools for the comparison of microbial communities using phylogenetic information. It takes as input a single phylogenetic tree that contains sequences derived from at least two different environmental samples and a file describing which sequences came from which sample. | microbiome, comparison, microbial community, phylogenetic tree, sequence | is listed by: Human Microbiome Project | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014616 | 2025-04-02 11:10:30 | 822 | ||||||||||
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Metapath Resource Report Resource Website 10+ mentions |
Metapath (RRID:SCR_014621) | software application, data processing software, data analysis software, software resource | A statistical package for comparing metagenomic data-sets at the pathway level. It relies on a combination of metagenomic sequence data and prior metabolic pathway knowledge, which is pulled from KEGG. | microbiome, statistics, metagenomics, pathway, sequence, comaprison | is listed by: Human Microbiome Project | Available for download | SCR_014621 | 2025-04-02 11:10:31 | 14 | ||||||||||
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GapCloser Resource Report Resource Website 500+ mentions |
GapCloser (RRID:SCR_015026) | data analysis software, software application, sequence analysis software, software resource, source code, data processing software | Module of SOAPdenovo2 commonly used independently to close gaps in genome assemblies. | gap closure, genome assembly, sequence | is listed by: SOAP | PMID:23587118 | Free, Available for download | SCR_015026 | 2025-04-02 11:10:49 | 661 | |||||||||
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RNA22 Resource Report Resource Website 100+ mentions |
RNA22 (RRID:SCR_016507) | RNA22 | data analysis software, sequence analysis software, software application, software resource, data processing software | Software tool as a pattern based algorithm for detecting microRNA binding sites and their corresponding microRNA and mRNA complexes. Allows interactive exploration and visualization of miRNA target predictions. Permits link-out to external expression repositories and databases. | pattern, based, detecting, microRNA, binding, site, complex, sequence, genome, analysis, FASEB list | is listed by: OMICtools | A Star ; Singapore ; NIDDK DK04763; NIH AI54973 |
Free, Available for download, Freely available | SCR_016507 | RiboNucleic Acid 22 | 2025-04-02 11:12:22 | 181 | |||||||
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DINIES Resource Report Resource Website 1+ mentions |
DINIES (RRID:SCR_016505) | DINIES | data analysis software, software application, sequence analysis software, software resource, data processing software, web application | Web server for predicting unknown drug-target interaction networks from various types of biological data in the framework of supervised network inference. | predict, drug, target, interaction, network, biological, data, chemical, structure, protein, amino acid, sequence, domain, bio.tools |
is listed by: GenomeNet is listed by: Debian is listed by: bio.tools is related to: KEGG has parent organization: Kyoto University; Kyoto; Japan |
Ministry of Education ; Culture ; Sports ; Science and Technology of Japan ; the Japan Science and Technology Agency ; the Japan Society for the Promotion of Science |
PMID:24838565 | Free, Freely available | biotools:dinies | https://bio.tools/dinies | SCR_016505 | Drug target Interaction Network Inference Engine based on Supervised analysis | 2025-04-02 11:12:22 | 3 | ||||
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Jpred Resource Report Resource Website 100+ mentions |
Jpred (RRID:SCR_016504) | data analysis software, software application, sequence analysis software, data analytics software, software resource, data processing software | Software tool for protein secondary structure prediction from the amino acid sequence by the JNet algorithm. Makes also predictions on Solvent Accessibility and Coiled-coil regions. | protein, secondary, structure, prediction, amino, acid, sequence, accurate, JNet algorithm, solvent, accessibility, coiled, coil, region | Biotechnology and Biological Sciences Research Council ; Wellcome Trust 355804783; Wellcome Trust WT092340; Wellcome Trust WT083481; Wellcome Trust 106370Z14 |
DOI:10.1093/nar/gkn238 | Free, Available for download, Freely available,Tutorial available | SCR_016504 | Jprotein secondary structure PREDiction | 2025-04-02 11:12:22 | 120 | ||||||||
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NAT/NCS2 Hound Resource Report Resource Website 1+ mentions |
NAT/NCS2 Hound (RRID:SCR_016473) | NAT, NCS2 | data analysis software, software application, sequence analysis software, software resource, data processing software, web application | Web server for the detection and evolutionary classification of prokaryotic and eukaryotic nucleobase-cation symporters of the NAT/NCS2 family. Used to scan, identify and evolutionary classify NAT/NCS2 nucleobase transporter proteins. | protein, sequence, scan, identify, evolutionary, classify, prokaryotic, nucleobase, transporter, protein, amino acid, conserved |
is listed by: OMICtools has parent organization: University of Thessaly; Thessaly; Greece |
DOI:10.1101/332452 | Free, Available to download, Freely available | SCR_016473 | Nucleobase Ascorbate Transporter, NCS2:Nucleobase Cation Symporter 2 | 2025-04-02 11:12:21 | 1 | |||||||
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1000 Fungal Genome Project Resource Report Resource Website 1+ mentions |
1000 Fungal Genome Project (RRID:SCR_016463) | topical portal, portal, database, data access protocol, project portal, data or information resource, organism-related portal, web service, software resource | Web application to provide genomic information for fungi. Includes sequenced fungal genomes, those in progress, and selected nominations. Nomination of new species for genome sequencing in the families or only one reference genome possible after providing DNA/RNA samples for their sequencing. Used to explore the diversity of fungi important for energy and the environment. | project, genomic, information, fungi, data, sequence, energy, environment |
is related to: MycoCosm is related to: Lawrence Berkeley National Laboratory has parent organization: DOE Joint Genome Institute |
the DOE Office of Biological and Environmental Research (BER) | Free, Register for an account | SCR_016463 | 2025-04-02 11:12:21 | 2 | |||||||||
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MentaLiST Resource Report Resource Website 1+ mentions |
MentaLiST (RRID:SCR_016469) | data analysis software, sequence analysis software, software application, software resource, data processing software | Software for a MLST (multi-locus sequence typing) caller, based on a k-mer counting algorithm and written in the Julia language. Designed and implemented to handle large typing schemes. | next, generation, sequencing, multi, locus, sequence, typing, pathogen, surveillance, gene, identify, strain, type, housekeeping, whole, genome, sequencing, data, bacteria, genotyping, bio.tools |
is listed by: bio.tools is listed by: Debian |
Canadian Institute for Health Research ; Genome Canada ; Genome BC |
PMID:29319471 | Free, Available for download, Freely available | biotools:mentalist | https://bio.tools/mentalist | SCR_016469 | 2025-04-02 11:12:21 | 7 | ||||||
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Centrifuge Classifier Resource Report Resource Website 1+ mentions |
Centrifuge Classifier (RRID:SCR_016665) | data analysis software, sequence analysis software, software application, software resource, data processing software | Software for rapid and sensitive classification of metagenomic sequences. Used for the classification of DNA sequences from microbial samples and analysis of large metagenomics data sets on conventional desktop computers. | classification, large, metagenomic, sequence, DNA, microbial, sample, analysis, data, desktop, computer, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is related to: Pavian has parent organization: Center for Computational Biology at JHU |
U. S. Army Research Office W911NF1410490; NSF ABI1356078; NHGRI R01 HG006677; NIGMS R01 GM083873 |
DOI:10.1101/gr.210641.116 | Free, Available for download, Freely available | biotools:centrifuge, OMICS_12217 | https://github.com/infphilo/centrifuge https://bio.tools/centrifuge https://sources.debian.org/src/centrifuge/ |
SCR_016665 | 2025-04-02 11:12:27 | 7 | ||||||
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PaVE Resource Report Resource Website 100+ mentions |
PaVE (RRID:SCR_016599) | PaVE | analysis service resource, production service resource, database, data analysis service, service resource, data or information resource, software resource, web application | Collection of curated papillomavirus genomic sequences, accompanied by web-based sequence analysis tools. Database and web applications support the storage, annotation, analysis, and exchange of information. | data, curated, papilloma, virus, genomic, sequence, analysis, storage, annotation, FASEB list | is listed by: NIAID | NIAID ZIA AI001071 | PMID:28053164 | Open source | SCR_016599 | PapillomaVirus Episteme, Papillomavirus Episteme | 2025-04-02 11:12:25 | 108 | ||||||
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BLASTClust Resource Report Resource Website 50+ mentions |
BLASTClust (RRID:SCR_016641) | data analysis software, sequence analysis software, software application, software resource, data processing software | Software tool as a program within the standalone BLAST package used to cluster either protein or nucleotide sequences. Used to make non redundant sequence sets. | cluster, protein, nucleotide, sequence, pairwise, match, sequence |
is listed by: SoftCite has parent organization: NCBI works with: NCBI BLAST |
Free, Freely available | SCR_016641 | 2025-04-02 11:12:26 | 80 | ||||||||||
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Genotyping Resource Report Resource Website 10+ mentions |
Genotyping (RRID:SCR_016645) | data access protocol, data analysis software, software application, sequence analysis software, web service, software resource, data processing software | Web tool to identify the genotype of a viral sequence. A window is slid along the query sequence and each window is compared by BLAST to each of the reference sequences for a particular virus. | identify, genotype, viral, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: NCBI works with: NCBI BLAST |
Free, Freely available | biotools:ncbi_genotyping | https://bio.tools/ncbi_genotyping | SCR_016645 | 2025-04-02 11:12:26 | 27 | ||||||||
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Open Reading Frame Finder Resource Report Resource Website 1000+ mentions |
Open Reading Frame Finder (RRID:SCR_016643) | ORF finder | analysis service resource, production service resource, data analysis software, service resource, software application, sequence analysis software, software resource, data processing software | Software tool to search for open reading frames (ORFs) in the DNA sequence. The program returns the range of each ORF, along with its protein translation. Used to search newly sequenced DNA for potential protein encoding segments, verify predicted protein. Limited to the subrange of the query sequence up to 50 kb long. | search, open, reading, frame, DNA, sequence, ORF, protein, translation, data, encoding, segment, verify |
uses: BLASTP has parent organization: NCBI |
Free, Available for download, Freely available | SCR_016643 | Open Reading Frame finder, Open Reading Frame Finder | 2025-04-02 11:12:26 | 1281 | ||||||||
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Libra Resource Report Resource Website |
Libra (RRID:SCR_016608) | data analysis software, software application, sequence analysis software, data analytics software, software resource, data processing software | Hadoop based tool for massive comparative metagenomics analysis. Compute the similarity between metagenomic samples. | gene, distance, matrix, computation, k-mer-based, sequence, comparison, Hadoop, metagenomic, sample, bio.tools |
is listed by: bio.tools is listed by: Debian |
NSF 1640775 | Free, Available for download, Freely available | biotools:Libra_k-mer | https://bio.tools/Libra_k-mer | SCR_016608 | 2025-04-02 11:12:25 | 0 | |||||||
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CCTOP Resource Report Resource Website 10+ mentions |
CCTOP (RRID:SCR_016963) | CCTOP | analysis service resource, production service resource, data access protocol, service resource, web service, software resource | Web application providing transmembrane topology prediction. Server incorporates topology information from existing experimental and computational sources using the probabilistic framework of hidden Markov model. Provides the option to precede the topology prediction with signal peptide prediction and transmembrane globular protein discrimination. Given the amino acid sequence of a putative α helical transmembrane protein, CCTOP predicts its topology i.e. localization of membrane spanning regions and orientation of segments between them. | transmembrane, topology, prediction, signal, peptide, globular, protein, discrimination, amino, acid, sequence, region, orientation, segment, bio.tools |
is listed by: Debian is listed by: bio.tools works with: PDBTM works with: Topology Data Bank of Transmembrane Proteins works with: TopDom |
Hungarian Scientific Research Fund | PMID:25943549 | Free, Freely available | biotools:cctop | https://bio.tools/cctop | SCR_016963 | CCTOP, Consensus Constrained TOPology | 2025-04-02 11:12:34 | 29 | ||||
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ALGGEN-PROMO Resource Report Resource Website 100+ mentions |
ALGGEN-PROMO (RRID:SCR_016926) | laboratory portal, portal, data analysis software, organization portal, data or information resource, service resource, software application, sequence analysis software, software resource, data processing software | Web tool to identify putative transcription factor binding sites (TFBS) in DNA sequences from a species or groups of species of interest. Used for detection of known transcription regulatory elements using species-tailored searches. | identify, transcription, factor, binding, site, DNA, sequence, species, regulatory, element, search | PMID:11847087 PMID:12824386 |
Free, Available for download, Freely available | SCR_016926 | PROMO, ALGorithmics and GENetics PROMO, ALGGEN, ALGGEN-PROMO | 2025-04-02 11:12:33 | 322 | |||||||||
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smMIPfil Resource Report Resource Website 1+ mentions |
smMIPfil (RRID:SCR_016892) | software application, data processing software, data analysis software, software resource | Software tool for single molecule Molecular Inversion Probes data analysis. This is a stand-alone perl script. Except that this is dependent on the samtools, no installation required. | nucleotide, DNA, read, unique, molecular, identifier, single, inversion, probe, data, analysis, mutation, sequence | requires: SAMTOOLS | Free, Available for download, Freely available | SCR_016892 | single molecule Molecular Inversion Probesfil, smMIPfil | 2025-04-02 11:12:32 | 2 | |||||||||
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CRISPR-P Resource Report Resource Website 10+ mentions |
CRISPR-P (RRID:SCR_016941) | analysis service resource, production service resource, data access protocol, service resource, web service, software resource | Web tool for synthetic single-guide RNA design of CRISPR-system in plants. Allows to search for high specificity Cas9 target sites within DNA sequences of interest, which also provides off-target loci prediction for specificity analyses and marks restriction enzyme cutting site to every sgRNA for further convenient in experiment. | synthetic, single, RNA, CRISP, plant, Cas9, target, DNA, sequence, analysis, restriction, enzyme, sgRNA, bio.tools |
is listed by: Debian is listed by: bio.tools |
National Basic Research Program of China ; Program for New Century Excellent Talents in University ; Fundamental Research Funds for the Central Universities |
PMID:24719468 | Free, Freely available | biotools:CRISPR-P | https://bio.tools/CRISPR-P | SCR_016941 | CRISPR-P 2.0, Clustered Regularly Interspaced Short Palindromic Repeats P, CRISPR P | 2025-04-02 11:12:33 | 27 |
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