Genome Annotation

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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 Science 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 CD-ROM.

Modern Genome Annotation

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Author : D. Frishman
language : en
Publisher: Springer Science & Business Media
Release Date : 2009-10-02

Modern Genome Annotation written by D. Frishman and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009-10-02 with Science categories.

An accurate description of current scientific developments in the field of bioinformatics and computational implementation is presented by research of the BioSapiens Network of Excellence. Bioinformatics is essential for annotating the structure and function of genes, proteins and the analysis of complete genomes and to molecular biology and biochemistry. Included is an overview of bioinformatics, the full spectrum of genome annotation approaches including; genome analysis and gene prediction, gene regulation analysis and expression, genome variation and QTL analysis, large scale protein annotation of function and structure, annotation and prediction of protein interactions, and the organization and annotation of molecular networks and biochemical pathways. Also covered is a technical framework to organize and represent genome data using the DAS technology and work in the annotation of two large genomic sets: HIV/HCV viral genomes and splicing alternatives potentially encoded in 1% of the human genome.

Intelligent Systems For Genome Functional Annotations

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Author : Shandar Ahmad
language : en
Publisher: Frontiers Media SA
Release Date : 2020-10-23

Intelligent Systems For Genome Functional Annotations written by Shandar Ahmad and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-10-23 with Technology & Engineering categories.

This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact.

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 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.

Database Annotation In Molecular Biology

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Author : Arthur M. Lesk
language : en
Publisher: John Wiley & Sons
Release Date : 2005-09-01

Database Annotation In Molecular Biology written by Arthur M. Lesk and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2005-09-01 with Medical categories.

Two factors dominate current molecular biology: the amount of raw data is increasing very rapidly and successful applications in biomedical research require carefully curated and annotated databases. The quality of the experimental data -- especially nucleic acid sequences -- is satisfactory; however, annotations depend on features inferred from the data rather than measured directly, for instance the identification of genes in genome sequences. It is essential that these inferences are as accurate as possible and this requires human intervention. With the recognition of the importance of accurate database annotation and the requirement for individuals with particular constellations of skills to carry it out, annotators are emerging as specialists within the profession of bioinformatics. This book compiles information about annotation -- its current status, what is required to improve it, what skills must be brought to bear on database curation and hence what is the proper training for annotators. The book should be essential reading for all people working on biological databases, both biologists and computer scientists. It will also be of interest to all users of such databases, including molecular biologists, geneticists, protein chemists, clinicians and drug developers.

Egasp 05

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Author : Roderic Guigó
language : en
Publisher: Biomed Central Limited
Release Date : 2006

Egasp 05 written by Roderic Guigó and has been published by Biomed Central Limited this book supported file pdf, txt, epub, kindle and other format this book has been release on 2006 with Science categories.

Articles in EGASP '05 are based on presentations made at the E-GASP 2005 gene prediction workshop, held in Hinxton, UK, on 6-7 May 2005. The workshop was community experiment to assess the state-of-the-art in genome annotation in the human genome, with the goal of assessing the accuracy of computational methods to predict protein coding genes in DNA and the overall assessment of the completeness of the current human genome annotations.

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.

Genome Annotation Using Average Mutual Information

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Author : Garin P. Newcomb
language : en
Publisher:
Release Date : 2021

Genome Annotation Using Average Mutual Information written by Garin P. Newcomb and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021 with categories.

Advancements in high-throughput DNA sequencing technologies and ambitious goals for their use are resulting in the generation of a deluge of unannotated sequenced genomes. This makes computational tools that can aid in annotation increasingly valuable. Here, we provide a detailed exploration of the utility as well as the limitations of average mutual information (AMI) in several steps of genome annotation. For a genomic sequence, AMI is a measure of the information a base contains about the base separated by a fixed lag. A profile is constructed by calculating AMI at multiple lags. In addition to traditional AMI, we employ two AMI variants: expanded AMI and expanded-adjusted AMI, both of which preserve some granular detail discarded by AMI. First, we demonstrate AMI’s capacity to assess evolutionary similarity by constructing phylogenetic trees similar to those currently accepted. The remainder of this work focuses on applications involving binary classification. We use support vector machines trained using the AMI profiles to classify sequences and evaluate predictive performance. These classification problems include predicting whether sequences come from protein-coding regions, identifying essential genes, and making functional predictions about the proteins genes produce. We conclude that AMI is particularly adept at identifying coding regions, and this behavior is consistent for species across all of life’s diversity.

Genesmith

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Author : Ravi Dandekar
language : en
Publisher:
Release Date : 2016

Genesmith written by Ravi Dandekar and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016 with categories.

Modern gene prediction, otherwise known as ab initio gene annotation, has yet to progress to a level of accuracy where it can replace the more costly process of manual curation through laboratory experiments. Gene annotation software utilizes machine learning approaches to model genes using Hidden Markov Models (HMMs) in order to accurately predict the location and structure of genes in a given genome. To gain a more cohesive understanding of which components can be improved in gene prediction algorithms, we developed flexible gene annotation software, Genesmith, in order to experiment with different HMM structures. Our results show that reducing the complexity of gene HMMs may reduce the overall accuracy of gene prediction, but there are certain features, such as donor and acceptor splice sites in introns, which remain highly predictive. In addition to our findings, we also introduce a new decoding algorithm, the Stochastic Viterbi, for extracting gene structure from genomic sequence. Our results point out holes in the current ab initio gene annotation process and suggest potential avenues for improvement.