Genome Annotation
Genome annotation for clinical genomic diagnostics: strengths and weaknesses
... Genome annotation is also increasingly seen as essen- tial for the development of pharmacological interven- tions, such as drug design. Typically, drug design targets the main transcript of a gene (the ...
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EMBLmyGFF3: a converter facilitating genome annotation submission to European Nucleotide Archive
... different annotation tools ...the annotation of two Candida intermedia strains performed with the genome annotation pipeline MAKER [15], as well as the annotation of Ectocarpus ...
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Genome Annotation of Meloidogyne hapla.
... or genome annotation; rather, it is better suited as one of several supporting pillars of evidence or in the collection of small-scale gene training ...of annotation dimensions depending on the ...
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Improving the Caenorhabditis elegans Genome Annotation Using Machine Learning
... precise genome annotations are of prime importance, as they allow the accurate definition of genic ...the genome annotation of the nematode Caenorhabditis ...elegans genome annotation ...
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Genome Annotation and Comparative Genomics of ORF Virus
... By genome annotation, an individual gene and its protein (or RNA) product can be predicted by in depth analysis of several gene features, such as ORFs length, % (G + C) content, promoter, polyA tail, ...
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Solving the Problem: Genome Annotation Standards before the Data Deluge
... a genome indi- cating that their presence is a recent evolutionary event ...all genome annotation should reflect the biology as determined by the underly- ing ...in genome records (Table ...
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Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs)
... Functional annotation of genomes is a critical aspect of the genomics ...new genome sequences are plainly ...for genome annotation is the sequence database search, the results of which allow ...
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The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)
... for annotation needs to be associated with an analysis project that has already been specified in the Genomes OnLine Database ...Microbial genome annotation consists of three stages: sequence data ...
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Analysis of 14 BAC Sequences from the Aedes Aegypti Genome: A Benchmark for Genome Annotation and Assembly
... In silico gene prediction was performed initially on the raw assembled scaffolds. A preliminary (BLASTX) analysis of these predicted transcripts (data not shown) demonstrated that there was a significant amount of ...
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Full length messenger RNA sequences greatly improve genome annotation
... The alignments generated from the cDNA sequences were used to create new gene models for the corresponding genes in the A. thaliana genome. Many of the genes have been manually curated, but many others were ...
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An Updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3
... the genome of Ruegeria pomeroyi DSS-3 was published in 2004, it represented the first sequence from a heterotrophic marine ...this genome remains useful, we have updated 69 genes to incorporate functional ...
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Toward a standard in structural genome annotation for prokaryotes
... A test set of genomes with varying GC% was identified and the gene calls for GeneMarkS [9], Glimmer3 [10], and Prodigal [11], which are the three most popular ab initio methods, were obtained from RefSeq’s public ftp ...
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Genomic Resources for Gene Discovery, Functional Genome Annotation, and Evolutionary Studies of Maize and Its Close Relatives
... smaller genome size (730 Mb), sorghum became a model for research related to maize (Bennetzen and Freeling 1993), including C4 and drought tolerance research (Paterson et ...draft genome sequence of sorghum ...
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The past, present and future of genome wide re annotation
... a genome to produce a ‘better’ result, which can easily be obtained by loosening the criteria for function prediction - for example by using a weaker threshold for sequence- similarity ...for genome ...
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Coordinated international action to accelerate genome to phenome with FAANG, the Functional Annotation of Animal Genomes project
... using genome information to predict such complex outcomes, whether it is the efficacy of a drug, susceptibility to can- cer, or the performance of the daughters of an elite dairy ...by genome sequence ...
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Genome sequencing, annotation and analysis of Salmonella enterica sub species salamae strain DMA-1
... Whole genome annotation at RAST server shows that Salmonella enterica, subspecies salamae strain DMA- 1 contains genes related to the virulence, disease, defense and adhesion; mediator of hyperadherence ...
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Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium
... the annotation of a gene product in the Brown et ...automated annotation, highlighting the importance of manual curation where ...al. genome annotation is provided in Additional file ...
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Genome scaffolding and annotation for the pathogen vector Ixodes ricinus by ultra long single molecule sequencing
... its genome is crucial. Genome coding sequences pave the way for comprehensive proteomic and transcriptomic ...and genome annotation warrant functional analyses, potentially revealing new ...
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Genome sequencing, annotation and comparative genomic analysis of Shigella dysenteriae strain SD1D
... (Rapid Annotation using Subsystem Technology) system. Final genome draft was employed for genome annotation using RAST server and RNAmmer ...
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Annotation inconsistencies beyond sequence similarity-based function prediction – phylogeny and genome structure
... We are poised to explore this approach further and, sub- ject to adequate support, plan to automate the validation process of function prediction with additional elements at genome/transcriptome/variome/proteome ...
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