A Systematic Annotation Package
Names
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A Systematic Annotation Package
metasource: Fairsharing.org
version: FAIRsharing.org: ASAP; A Systematic Annotation Package; DOI: https://doi.org/10.25504/FAIRsharing.anpa6; Last edited: Dec. 19, 2019, 11:21 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
ASAP
metasource: Fairsharing.org
version: FAIRsharing.org: ASAP; A Systematic Annotation Package; DOI: https://doi.org/10.25504/FAIRsharing.anpa6; Last edited: Dec. 19, 2019, 11:21 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: re3data.org
version: re3data.org: ASAP; editing status 2017-06-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CG7P last accessed: 2022-11-04
A systematic annotation package for community analysis of genomes
metasource: re3data.org
version: re3data.org: ASAP; editing status 2017-06-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CG7P last accessed: 2022-11-04
Names
More detailed information about this field from each metasource.
A Systematic Annotation Package
metasource: Fairsharing.orgversion: FAIRsharing.org: ASAP; A Systematic Annotation Package; DOI: https://doi.org/10.25504/FAIRsharing.anpa6; Last edited: Dec. 19, 2019, 11:21 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
ASAP
metasource: Fairsharing.orgversion: FAIRsharing.org: ASAP; A Systematic Annotation Package; DOI: https://doi.org/10.25504/FAIRsharing.anpa6; Last edited: Dec. 19, 2019, 11:21 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: re3data.org
version: re3data.org: ASAP; editing status 2017-06-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CG7P last accessed: 2022-11-04
A systematic annotation package for community analysis of genomes
metasource: re3data.orgversion: re3data.org: ASAP; editing status 2017-06-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CG7P last accessed: 2022-11-04
Other names: ASAP, A systematic annotation package for community analysis of genomes
Names
More detailed information about this field from each metasource.
A Systematic Annotation Package
metasource: Fairsharing.orgversion: FAIRsharing.org: ASAP; A Systematic Annotation Package; DOI: https://doi.org/10.25504/FAIRsharing.anpa6; Last edited: Dec. 19, 2019, 11:21 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
ASAP
metasource: Fairsharing.orgversion: FAIRsharing.org: ASAP; A Systematic Annotation Package; DOI: https://doi.org/10.25504/FAIRsharing.anpa6; Last edited: Dec. 19, 2019, 11:21 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: re3data.org
version: re3data.org: ASAP; editing status 2017-06-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CG7P last accessed: 2022-11-04
A systematic annotation package for community analysis of genomes
metasource: re3data.orgversion: re3data.org: ASAP; editing status 2017-06-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CG7P last accessed: 2022-11-04
ASAP is a relational database and web interface developed to store, update and distribute genome sequence data and gene expression data. It was designed to facilitate ongoing community annotation of genomes and to grow with genome projects as they move from the preliminary data stage through post-sequencing functional analysis.
Description
More detailed information about this field from each metasource.
ASAP is a relational database and web interface developed to store, update and distribute genome sequence data and gene expression data. It was designed to facilitate ongoing community annotation of genomes and to grow with genome projects as they move from the preliminary data stage through post-sequencing functional analysis.
metasource: Fairsharing.orgversion: FAIRsharing.org: ASAP; A Systematic Annotation Package; DOI: https://doi.org/10.25504/FAIRsharing.anpa6; Last edited: Dec. 19, 2019, 11:21 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
ASAP (a systematic annotation package for community analysis of genomes) is a relational database and web interface developed to store, update and distribute genome sequence data and gene expression data collected by or in collaboration with researchers at the University of Wisconsin - Madison. ASAP was designed to facilitate ongoing community annotation of genomes and to grow with genome projects as they move from the preliminary data stage through post-sequencing functional analysis. The ASAP database includes multiple genome sequences at various stages of analysis, and gene expression data from preliminary experiments.
metasource: re3data.orgversion: re3data.org: ASAP; editing status 2017-06-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CG7P last accessed: 2022-11-04
Webpage:
http://asap.genetics.wisc.edu/asap/home.phpWebpage
More detailed information about this field from each metasource.
http://asap.genetics.wisc.edu/asap/home.php
metasource: Fairsharing.orgversion: FAIRsharing.org: ASAP; A Systematic Annotation Package; DOI: https://doi.org/10.25504/FAIRsharing.anpa6; Last edited: Dec. 19, 2019, 11:21 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
https://asap.ahabs.wisc.edu/asap/home.php
metasource: re3data.orgversion: re3data.org: ASAP; editing status 2017-06-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CG7P last accessed: 2022-11-04
Licence:
Name: CopyrightsLicence name
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Copyrights
metasource: re3data.orgversion: re3data.org: ASAP; editing status 2017-06-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CG7P last accessed: 2022-11-04
Licence URL
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https://www.wisconsin.edu/general-counsel/legal-topics/copyright/
metasource: re3data.orgversion: re3data.org: ASAP; editing status 2017-06-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CG7P last accessed: 2022-11-04
Publications:
Publications
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ASAP, a systematic annotation package for community analysis of genomes
PMID: 12519969
metasource: Fairsharing.org
version: FAIRsharing.org: ASAP; A Systematic Annotation Package; DOI: https://doi.org/10.25504/FAIRsharing.anpa6; Last edited: Dec. 19, 2019, 11:21 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
Publications
More detailed information about this field from each metasource.
ASAP, a systematic annotation package for community analysis of genomes
PMID: 12519969
metasource: Fairsharing.org
version: FAIRsharing.org: ASAP; A Systematic Annotation Package; DOI: https://doi.org/10.25504/FAIRsharing.anpa6; Last edited: Dec. 19, 2019, 11:21 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
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ASAP, a systematic annotation package for community analysis of genomes
PubMed citations: 85.
85 articles citing: ASAP, a systematic annotation package for community analysis of genomes
Species of Dickeya and Pectobacterium Isolated during an Outbreak of Blackleg and Soft Rot of Potato in Northeastern and North Central United States. PMID:34442812
Proline codon pair selection determines ribosome pausing strength and translation efficiency in bacteria. PMID:34002016
Complete Genome Sequence of the Necrotrophic Plant-Pathogenic Bacterium Pectobacterium brasiliense 1692. PMID:32193231
Comparative Genome Analysis of Uropathogenic Morganella morganii Strains. PMID:31231616
Genomic characterisation of the new Dickeya fangzhongdai species regrouping plant pathogens and environmental isolates. PMID:30634913
Evolutionary analysis of polyproline motifs in Escherichia coli reveals their regulatory role in translation. PMID:29389943
Discovering missing reactions of metabolic networks by using gene co-expression data. PMID:28150713
Genome-Wide Transcriptional Regulation and Chromosome Structural Arrangement by GalR in E. coli. PMID:27900321
Bioinformatics Analysis of the Complete Genome Sequence of the Mango Tree Pathogen Pseudomonas syringae pv. syringae UMAF0158 Reveals Traits Relevant to Virulence and Epiphytic Lifestyle. PMID:26313942
Web resources for model organism studies. PMID:25707592
GenoBase: comprehensive resource database of Escherichia coli K-12. PMID:25399415
Transcriptome-based analysis of the Pantoea stewartii quorum-sensing regulon and identification of EsaR direct targets. PMID:25015891
Identification of host-microbe interaction factors in the genomes of soft rot-associated pathogens Dickeya dadantii 3937 and Pectobacterium carotovorum WPP14 with supervised machine learning. PMID:24952641
Metabolite changes signal genetic regulatory mechanisms for robust cell behavior. PMID:24473130
Dynamic transcriptional response of Escherichia coli to inclusion body formation. PMID:24338599
Transcriptome changes associated with anaerobic growth in Yersinia intermedia (ATCC29909). PMID:24116118
Proteomic analysis of the quorum-sensing regulon in Pantoea stewartii and identification of direct targets of EsaR. PMID:23913428
Analysis of the Lactobacillus casei supragenome and its influence in species evolution and lifestyle adaptation. PMID:23035691
Noncoding RNAs binding to the nucleoid protein HU in Escherichia coli. PMID:22942248
The bacterium Pantoea stewartii uses two different type III secretion systems to colonize its plant host and insect vector. PMID:22773631
Evolution of the metabolic and regulatory networks associated with oxygen availability in two phytopathogenic enterobacteria. PMID:22439737
EcoliWiki: a wiki-based community resource for Escherichia coli. PMID:22064863
The 3-hydroxy-2-butanone pathway is required for Pectobacterium carotovorum pathogenesis. PMID:21876734
Pantoea stewartii subsp. stewartii: lessons learned from a xylem-dwelling pathogen of sweet corn. PMID:21726365
Genome sequence of the plant-pathogenic bacterium Dickeya dadantii 3937. PMID:21217001
An automated phenotype-driven approach (GeneForce) for refining metabolic and regulatory models. PMID:21060853
Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis. PMID:20876091
Patterns of subnet usage reveal distinct scales of regulation in the transcriptional regulatory network of Escherichia coli. PMID:20617198
Flux balance analysis accounting for metabolite dilution. PMID:20398381
Strategies for enhanced annotation of a microarray probe set. PMID:20223738
Purification and characterization of the folate catabolic enzyme p-aminobenzoyl-glutamate hydrolase from Escherichia coli. PMID:20190044
Cellular stress created by intermediary metabolite imbalances. PMID:19887636
A subset of the diverse COG0523 family of putative metal chaperones is linked to zinc homeostasis in all kingdoms of life. PMID:19822009
SlyA, a MarR family transcriptional regulator, is essential for virulence in Dickeya dadantii 3937. PMID:19542281
Text-mining of PubMed abstracts by natural language processing to create a public knowledge base on molecular mechanisms of bacterial enteropathogens. PMID:19515247
Gene expression profiling and the use of genome-scale in silico models of Escherichia coli for analysis: providing context for content. PMID:19363119
Biochemical and Genetic Characterization of PspE and GlpE, Two Single-domain Sulfurtransferases of Escherichia coli. PMID:19088907
sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes. PMID:19015153
The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse. PMID:18245285
Mosquito transcriptome changes and filarial worm resistance in Armigeres subalbatus. PMID:18088420
Construction and characterization of an expressed sequenced tag library for the mosquito vector Armigeres subalbatus. PMID:18088419
EuCAP, a Eukaryotic Community Annotation Package, and its application to the rice genome. PMID:17961238
Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata. PMID:17932051
Manual curation is not sufficient for annotation of genomic databases. PMID:17646325
The correlation between architecture and mRNA abundance in the genetic regulatory network of Escherichia coli. PMID:17640329
Using gene expression data and network topology to detect substantial pathways, clusters and switches during oxygen deprivation of Escherichia coli. PMID:17488495
On kinetics of phage adsorption. PMID:17434950
An assessment of the role of DNA adenine methyltransferase on gene expression regulation in E coli. PMID:17342207
Escherichia coli abg genes enable uptake and cleavage of the folate catabolite p-aminobenzoyl-glutamate. PMID:17307853
The trans-envelope Tol-Pal complex is part of the cell division machinery and required for proper outer-membrane invagination during cell constriction in E. coli. PMID:17233825
Systems approach to refining genome annotation. PMID:17088549
Detection of prokaryotic promoters from the genomic distribution of hexanucleotide pairs. PMID:17014715
Experimental and computational assessment of conditionally essential genes in Escherichia coli. PMID:17012394
Nucleotide sequence analysis of the enteropathogenic Escherichia coli adherence factor plasmid pMAR7. PMID:16926437
G-InforBIO: integrated system for microbial genomics. PMID:16887044
yrGATE: a web-based gene-structure annotation tool for the identification and dissemination of eukaryotic genes. PMID:16859520
AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system. PMID:16855290
The life-cycle of operons. PMID:16789824
A regression-based K nearest neighbor algorithm for gene function prediction from heterogeneous data. PMID:16723004
Global transcriptome response of recombinant Escherichia coli to heat-shock and dual heat-shock recombinant protein induction. PMID:16680459
Discovering functional gene expression patterns in the metabolic network of Escherichia coli with wavelets transforms. PMID:16524469
Systematic analysis of conservation relations in Escherichia coli genome-scale metabolic network reveals novel growth media. PMID:16461408
Escherichia coli K-12: a cooperatively developed annotation snapshot--2005. PMID:16397293
Whole-genome plasticity among Mycobacterium avium subspecies: insights from comparative genomic hybridizations. PMID:16385061
ASAP: a resource for annotating, curating, comparing, and disseminating genomic data. PMID:16381899
Intracellular screen to identify metagenomic clones that induce or inhibit a quorum-sensing biosensor. PMID:16204555
Identification and characterization of the fibrinogen-like domain of fibrinogen-related proteins in the mosquito, Anopheles gambiae, and the fruitfly, Drosophila melanogaster, genomes. PMID:16150145
Systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops. PMID:16011797
Differential gene expression for investigation of Escherichia coli biofilm inhibition by plant extract ursolic acid. PMID:16000817
Predicting non-coding RNA genes in Escherichia coli with boosted genetic programming. PMID:15942029
Characterization of two new aminopeptidases in Escherichia coli. PMID:15901689
Gene fusions and gene duplications: relevance to genomic annotation and functional analysis. PMID:15757509
Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation. PMID:15608211
EchoBASE: an integrated post-genomic database for Escherichia coli. PMID:15608209
Pyrosequencing: sequence typing at the speed of light. PMID:15477652
Genome image programs: visualization and interpretation of Escherichia coli microarray experiments. PMID:15342544
Description of the transcriptomes of immune response-activated hemocytes from the mosquito vectors Aedes aegypti and Armigeres subalbatus. PMID:15213157
PeerGAD: a peer-review-based and community-centric web application for viewing and annotating prokaryotic genome sequences. PMID:15184545
The Ensembl analysis pipeline. PMID:15123589
GenProtEC: an updated and improved analysis of functions of Escherichia coli K-12 proteins. PMID:14681418
Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome. PMID:14627830
Genome-scale analysis of the uses of the Escherichia coli genome: model-driven analysis of heterogeneous data sets. PMID:14563874
Reconciling gene expression data with known genome-scale regulatory network structures. PMID:14559784
A genomic perspective on nutrient provisioning by bacterial symbionts of insects. PMID:14527994
The biphenyl- and 4-chlorobiphenyl-catabolic transposon Tn4371, a member of a new family of genomic islands related to IncP and Ti plasmids. PMID:12902278
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gene expression data
metasource: Fairsharing.org
version: FAIRsharing.org: ASAP; A Systematic Annotation Package; DOI: https://doi.org/10.25504/FAIRsharing.anpa6; Last edited: Dec. 19, 2019, 11:21 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
genome
metasource: Fairsharing.org
version: FAIRsharing.org: ASAP; A Systematic Annotation Package; DOI: https://doi.org/10.25504/FAIRsharing.anpa6; Last edited: Dec. 19, 2019, 11:21 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
dna
metasource: re3data.org
version: re3data.org: ASAP; editing status 2017-06-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CG7P last accessed: 2022-11-04
chromosome
metasource: re3data.org
version: re3data.org: ASAP; editing status 2017-06-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CG7P last accessed: 2022-11-04
genetic mapping
metasource: re3data.org
version: re3data.org: ASAP; editing status 2017-06-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CG7P last accessed: 2022-11-04
genomics
metasource: re3data.org
version: re3data.org: ASAP; editing status 2017-06-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CG7P last accessed: 2022-11-04
nucleotides
metasource: re3data.org
version: re3data.org: ASAP; editing status 2017-06-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CG7P last accessed: 2022-11-04
protein
metasource: re3data.org
version: re3data.org: ASAP; editing status 2017-06-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CG7P last accessed: 2022-11-04
Tags
More detailed information about this field from each metasource.
gene expression data
metasource: Fairsharing.orgversion: FAIRsharing.org: ASAP; A Systematic Annotation Package; DOI: https://doi.org/10.25504/FAIRsharing.anpa6; Last edited: Dec. 19, 2019, 11:21 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
genome
metasource: Fairsharing.orgversion: FAIRsharing.org: ASAP; A Systematic Annotation Package; DOI: https://doi.org/10.25504/FAIRsharing.anpa6; Last edited: Dec. 19, 2019, 11:21 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
dna
metasource: re3data.orgversion: re3data.org: ASAP; editing status 2017-06-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CG7P last accessed: 2022-11-04
chromosome
metasource: re3data.orgversion: re3data.org: ASAP; editing status 2017-06-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CG7P last accessed: 2022-11-04
genetic mapping
metasource: re3data.orgversion: re3data.org: ASAP; editing status 2017-06-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CG7P last accessed: 2022-11-04
genomics
metasource: re3data.orgversion: re3data.org: ASAP; editing status 2017-06-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CG7P last accessed: 2022-11-04
nucleotides
metasource: re3data.orgversion: re3data.org: ASAP; editing status 2017-06-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CG7P last accessed: 2022-11-04
protein
metasource: re3data.orgversion: re3data.org: ASAP; editing status 2017-06-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CG7P last accessed: 2022-11-04
gene expression genome dna chromosome genetic mapping genomics nucleotides protein
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