An Assessment Of Genome Annotation Tools And An Approach To Solving A Set Of Problems Form A Genome Sequencing Project
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An Assessment Of Genome Annotation Tools And An Approach To Solving A Set Of Problems Form A Genome Sequencing Project
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Author : George W. Hartzell
language : en
Publisher:
Release Date : 2001
An Assessment Of Genome Annotation Tools And An Approach To Solving A Set Of Problems Form A Genome Sequencing Project written by George W. Hartzell and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2001 with categories.
An Assessment Of Genome Annotation Tools And An Approach To Solving A Set Of Problems Form A Genome Sequencing Project
DOWNLOAD
Author : George W. Hartzell
language : en
Publisher:
Release Date : 2001
An Assessment Of Genome Annotation Tools And An Approach To Solving A Set Of Problems Form A Genome Sequencing Project written by George W. Hartzell and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2001 with categories.
Genome Annotation
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Author : Jung Soh
language : en
Publisher: CRC Press
Release Date : 2016-04-19
Genome Annotation written by Jung Soh and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-04-19 with Computers categories.
The success of individualized medicine, advanced crops, and new and sustainable energy sources requires thoroughly annotated genomic information and the integration of this information into a coherent model. A thorough overview of this field, Genome Annotation explores automated genome analysis and annotation from its origins to the challenges of next-generation sequencing data analysis. The book initially takes you through the last 16 years since the sequencing of the first complete microbial genome. It explains how current analysis strategies were developed, including sequencing strategies, statistical models, and early annotation systems. The authors then present visualization techniques for displaying integrated results as well as state-of-the-art annotation tools, including MAGPIE, Ensembl, Bluejay, and Galaxy. They also discuss the pipelines for the analysis and annotation of complex, next-generation DNA sequencing data. Each chapter includes references and pointers to relevant tools. As very few existing genome annotation pipelines are capable of dealing with the staggering amount of DNA sequence information, new strategies must be developed to accommodate the needs of today’s genome researchers. Covering this topic in detail, Genome Annotation provides you with the foundation and tools to tackle this challenging and evolving area. Suitable for both students new to the field and professionals who deal with genomic information in their work, the book offers two genome annotation systems on an accompanying downloadable resources.
Dissertation Abstracts International
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Author :
language : en
Publisher:
Release Date : 2008
Dissertation Abstracts International written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008 with Dissertations, Academic categories.
The Genome Channel And Genome Annotation Consortium
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Author :
language : en
Publisher:
Release Date : 1997
The Genome Channel And Genome Annotation Consortium written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 1997 with categories.
Human and model organism sequencing projects will soon be producing data at a rate which will require new methods and infrastructure for users to be able to effectively view and understand the data. A multi-institutional project was recently funded to provide large-scale analytical processing capabilities and the authors present the results of several pilot efforts related to this project. The goals of the project are as follows: provide an environment where annotation can be constructed based on multiple interoperable analysis tools and significant available computing power; provide an environment where characterization of long genomic sequence regions can be facilitated and analysis can maintained and updated over time; provide an interactive graphical environment where predictions, features and evidence from many tools can be combined by users into high-quality annotation and visualized by the community; provide high-throughput automated analysis methods which can be configured by genome centers for their use in constructing annotation and facilitating data submission; provide high-quality annotation to large genomic sequence regions which would otherwise go unannotated; and provide the community with the best sequence level view of genomes possible. The components of this system are a number of services, a broker that oversees the distribution and management of tasks and a data warehouse, with services implemented using distributed object technology. Multiple gene prediction is accomplished using several gene finding tools including the GRAIL-EST system and gene annotation from databases such as Genbank is also captured. The data warehouse supporting the Genome Channel view is updated daily by automated Internet agents and event triggers which facilitate analysis procedures.
Bioinformatics Research And Applications
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Author : Ion Mandoiu
language : en
Publisher: Springer
Release Date : 2007-08-06
Bioinformatics Research And Applications written by Ion Mandoiu and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007-08-06 with Science categories.
This book constitutes the refereed proceedings of the Third International Symposium on Bioinformatics Research and Applications, ISBRA 2007, held in Atlanta, GA, USA in May 2007. The 55 revised full papers presented together with three invited talks cover a wide range of topics, including clustering and classification, gene expression analysis, gene networks, genome analysis, motif finding, pathways, protein structure prediction, protein domain interactions, phylogenetics, and software tools.
Doe Genomics
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Author :
language : en
Publisher:
Release Date : 2005
Doe Genomics written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2005 with Genomics categories.
Genome Annotation And Finding Repetitive Dna Elements
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Author : Renu Rawat
language : en
Publisher:
Release Date : 2014-06-03
Genome Annotation And Finding Repetitive Dna Elements written by Renu Rawat and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-06-03 with categories.
Bachelor Thesis from the year 2014 in the subject Computer Science - Bioinformatics, grade: 8.26, Lovely Professional University, course: b.tech honors biotechnology, language: English, abstract: As the number of genomes sequenced is increasing at high rate, there is a need of gene prediction method which is quick, reliable, inexpensive. In such conditions, the computations tool will serve as an alternative to wet lab methods. The confidence level of annotation by the tool can be enhanced by preparing exhaustive training data sets. The aim is to develop a tool which will read data from a DNA sequence file in the fasta format and will annotate it. For this purpose Genome Database was used to retrieve the input data. PERL programming has been put to develop this tool for annotation. To increase the confidence level of annotation the data was validated from multiple sources. Perl script was written to find the promoter region, repeats, transcription factor binding site, base periodicity, and nucleotide frequency. The program written was also executed to identify repeats, poly (A) signals, CpG islands, ARS. The tool will annotate the DNA by predicting the gene structure based on the consensus sequences of important regulatory elements. The confidence level of annotation of the predicted gene, non-coding region, ARS, repeats etc. were checked by running test dataset. This test dataset was annotated data as reported by genome database and computational tools. Gene prediction of the non-coding regions as reported by genome database (SGD) were performed by existing tools; the regions identified as non-coding by these tools were then analyzed for presence of repeats. The BLAST was used to annotate on the basis of sequence similarity with the already annotated genes. GeneMark.hmm and FGENESH were used for gene prediction. In order to validate the predicted results, annotations of genome of Saccharomyces cerevisiae from SGD Database, and output of different computational
An Approach To Improved Microbial Eukaryotic Genome Annotation
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Author : Matthew Sarrasin
language : en
Publisher:
Release Date : 2017
An Approach To Improved Microbial Eukaryotic Genome Annotation written by Matthew Sarrasin and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017 with categories.
New sequencing technologies have considerably accelerated the rate at which genomic data is being generated. One ongoing challenge is the accurate structural annotation of those novel genomes once sequenced and assembled, in particular if the organism does not have close relatives with well-annotated genomes. Whole-transcriptome sequencing (RNA-Seq) and assembly-both of which share similarities to whole-genome sequencing and assembly, respectively-have been shown to dramatically increase the accuracy of gene annotation. Read coverage, inferred splice junctions and assembled transcripts can provide valuable information about gene structure. Several annotation pipelines have been developed to automate structural annotation by incorporating information from RNA-Seq, as well as protein sequence similarity data, with the goal of reaching the accuracy of an expert curator. Annotation pipelines follow a similar workflow. The first step is to identify repetitive regions to prevent misinformed sequence alignments and gene predictions. The next step is to construct a database of evidence from experimental data such as RNA-Seq mapping and assembly, and protein sequence alignments, which are used to inform the generalised Hidden Markov Models of gene prediction software. The final step is to consolidate sequence alignments and gene predictions into a high-confidence consensus set. Thus, automated pipelines are complex, and therefore susceptible to incomplete and erroneous use of information, which can poison gene predictions and consensus model building. Here, we present an improved approach to microbial eukaryotic genome annotation. Its conception was based on identifying and mitigating potential sources of error and bias that are present in available pipelines. Our approach has two main aspects. The first is to create a more complete and diverse set of extrinsic evidence to better inform gene predictions. The second is to use extrinsic evidence in tandem with predictions such that the influence of their respective biases in the consensus gene models is reduced. We benchmarked our new tool against three known pipelines, showing significant gains in gene, transcript, exon and intron sensitivity and specificity in the genome annotation of microbial eukaryotes.
Challenges And Opportunities Of Healthgrids
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Author : Vicente Hernández
language : en
Publisher: IOS Press
Release Date : 2006
Challenges And Opportunities Of Healthgrids written by Vicente Hernández and has been published by IOS Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2006 with Medical categories.
The contributions of this publication follow mainly five main topics: Medical Imaging on the Grid; Ethical, Legal and Privacy Issues on HealthGrids; Bioinformatics on the Grid; Knowledge Discovery on HealthGrids; and Medical Assessment and HealthGrid Applications. The maturity of the discipline of HealthGrids is clearly reflected on these subjects. There are more contributions related to two main application areas (Medical Imaging and Bioinformatics), confirming the analysis of the HealthGrid White Paper published last year, which outlined them as the two more promising areas for HealthGrids. Along with these two areas, the assessment on the results of HealthGrid applications, also focused by several contributions, denotes also the maturity of HealthGrids. Finally the other two areas (Knowledge Discovery and Ethical, Legal and Privacy Issues) focus on basic technologies which are very relevant for HealthGrids.