Skip to main content

Annotating New Genes

In Order to Read Online or Download Annotating New Genes Full eBooks in PDF, EPUB, Tuebl and Mobi you need to create a Free account. Get any books you like and read everywhere you want. Fast Download Speed ~ Commercial & Ad Free. We cannot guarantee that every book is in the library!

Annotating New Genes

Annotating New Genes Book
Author : Shizuka Uchida
Publisher : Elsevier
Release : 2012-08-06
ISBN : 1908818123
Language : En, Es, Fr & De

GET BOOK

Book Description :

In recent years, a number of academic and commercial software packages and databases have been developed for the analysis and screening of biological data; however, the usability of these data is compromised by so-called novel genes to which no biological function is assigned. Annotating new genes outlines an approach to the analysis of evolutionary-conserved, heart-enriched genes with unknown functions, offering a step-by-step description of the procedure from screening to validation. The book begins by offering an introduction to the databases and software available, before moving on to cover programming guidelines, including a specific case study on the use of C-It for in silico screening. The second half of the book offers a step-by-step guide to experimental validation concepts and procedures, as well as an overview of additional potential applications of this approach in the field of stem cells and tissue regeneration, before a concluding chapter summarises the concepts and theories presented. Focuses not only on screening but also on biological validations Provides details of databases and software (web interface) products for biologists with minimal computation skills Offers a step-by-step outline of the procedure involved

An Integrated Approach to Enhancing Functional Annotation of Sequences for Data Analysis of a Transcriptome

An Integrated Approach to Enhancing Functional Annotation of Sequences for Data Analysis of a Transcriptome Book
Author : Matthew Morritt Hindle
Publisher : Unknown
Release : 2012
ISBN : 0987650XXX
Language : En, Es, Fr & De

GET BOOK

Book Description :

Given the ever increasing quantity of sequence data, functional annotation of new gene sequences persists as being a significant challenge for bioinformatics. This is a particular problem for transcriptomics studies in crop plants where large genomes and evolutionarily distant model organisms, means that identifying the function of a given gene used on a microarray, is often a non-trivial task. Information pertinent to gene annotations is spread across technically and semantically heterogeneous biological databases. Combining and exploiting these data in a consistent way has the potential to improve our ability to assign functions to new or uncharacterised genes. Methods: The Ondex data integration framework was further developed to integrate databases pertinent to plant gene annotation, and provide data inference tools. The CoPSA annotation pipeline was created to provide automated annotation of novel plant genes using this knowledgebase. CoPSA was used to derive annotations for Affymetrix GeneChips available for plant species. A conjoint approach was used to align GeneChip sequences to orthologous proteins, and identify protein domain regions. These proteins and domains were used together with multiple evidences to predict functional annotations for sequences on the GeneChip. Quality was assessed with reference to other annotation pipelines. These improved gene annotations were used in the analysis of a time-series transcriptomics study of the differential responses of durum wheat varieties to water stress. Results and Conclusions: The integration of plant databases using the Ondex showed that it was possible to increase the overall quantity and quality of information available, and thereby improve the resulting annotation. Direct data aggregation benefits were observed, as well as new information derived from inference across databases. The CoPSA pipeline was shown to improve coverage of the wheat microarray compared to the NetAffx and BLAST2GO pipelines. Leverage of these annotations during the analysis of data from a transcriptomics study of the durum wheat water stress responses, yielded new biological insights into water stress and highlighted potential candidate genes that could be used by breeders to improve drought response.

Genome Annotation

Genome Annotation Book
Author : Jung Soh,Paul M.K. Gordon,Christoph W. Sensen
Publisher : CRC Press
Release : 2016-04-19
ISBN : 1439841187
Language : En, Es, Fr & De

GET BOOK

Book Description :

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.

Functional Annotation of Farm Animal Genomes

Functional Annotation of Farm Animal Genomes Book
Author : Hans Cheng,Amanda Jane Chamberlain,Elisabetta Giuffra,Christa Kuehn,Christopher K. Tuggle,Huaijun Zhou
Publisher : Frontiers Media SA
Release : 2021-12-20
ISBN : 2889718298
Language : En, Es, Fr & De

GET BOOK

Book Description :

Download Functional Annotation of Farm Animal Genomes book written by Hans Cheng,Amanda Jane Chamberlain,Elisabetta Giuffra,Christa Kuehn,Christopher K. Tuggle,Huaijun Zhou, available in PDF, EPUB, and Kindle, or read full book online anywhere and anytime. Compatible with any devices.

Modern Genome Annotation

Modern Genome Annotation Book
Author : D. Frishman,Alfonso Valencia
Publisher : Springer Science & Business Media
Release : 2009-10-02
ISBN : 3211751238
Language : En, Es, Fr & De

GET BOOK

Book Description :

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.

IMG ER

IMG ER Book
Author : Anonim
Publisher : Unknown
Release : 2009
ISBN : 0987650XXX
Language : En, Es, Fr & De

GET BOOK

Book Description :

A rapidly increasing number of microbial genomes are sequenced by organizations worldwide and are eventually included into various public genome data resources. The quality of the annotations depends largely on the original dataset providers, with erroneous or incomplete annotations often carried over into the public resources and difficult to correct. We have developed an Expert Review (ER) version of the Integrated Microbial Genomes (IMG) system, with the goal of supporting systematic and efficient revision of microbial genome annotations. IMG ER provides tools for the review and curation of annotations of both new and publicly available microbial genomes within IMG's rich integrated genome framework. New genome datasets are included into IMG ER prior to their public release either with their native annotations or with annotations generated by IMG ER's annotation pipeline. IMG ER tools allow addressing annotation problems detected with IMG's comparative analysis tools, such as genes missed by gene prediction pipelines or genes without an associated function. Over the past year, IMG ER was used for improving the annotations of about 150 microbial genomes.

Database Annotation in Molecular Biology

Database Annotation in Molecular Biology Book
Author : Arthur M. Lesk
Publisher : John Wiley & Sons
Release : 2005-09-01
ISBN : 0470856858
Language : En, Es, Fr & De

GET BOOK

Book Description :

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.

The Genus Yersinia

The Genus Yersinia  Book
Author : Robert D. Perry,Jacqueline D. Fetherston
Publisher : Springer Science & Business Media
Release : 2007-09-25
ISBN : 0387721231
Language : En, Es, Fr & De

GET BOOK

Book Description :

The 9th International Symposium on Yersinia was held in Lexington, Kentucky, USA on October 10-14, 2006. Over 250 Yersinia researchers from 18 countries gathered to present and discuss their research. In addition to 37 oral presentations, there were 150 poster presentations. This Symposium volume is based on selected presentations from the meeting and contains both reviews and research articles. It is divided into six topic areas: 1) genomics; 2) structure and metabolism; 3) regulatory mechanisms; 4) pathogenesis and host interactions; 5) molecular epidemiology and detection; and 6) vaccine and antimicrobial therapy development. Consequently, this volume covers a wide range of current research areas in the Yersinia field.

Evolution of Fungi and Fungal Like Organisms

Evolution of Fungi and Fungal Like Organisms Book
Author : Stefanie Pöggeler,Johannes Wöstemeyer
Publisher : Springer Science & Business Media
Release : 2011-07-28
ISBN : 3642199747
Language : En, Es, Fr & De

GET BOOK

Book Description :

Based on sequence analyses of many different genes, the past decade has provided us with a profound knowledge of fungal systematics and phylogeny. In addition, a number of sequences of complete fungal genomes have been identified and several others will soon follow. In this volume, leading experts address questions concerning the origin of the fungal kingdom and fungal evolution at a level of analytical refinement that has never been possible before. The following major aspects are highlighted: evolutionary roots of fungi; evolution of signaling in fungi and fungal-like organisms; evolution of mutualistic systems and metabolism in fungi; and evolutionary mechanisms and trends.

Graph Drawing

Graph Drawing Book
Author : David Eppstein,Emden R Gansner
Publisher : Springer
Release : 2010-03-10
ISBN : 3642118054
Language : En, Es, Fr & De

GET BOOK

Book Description :

This volume constitutes the refereed proceedings of the 17th International Symposium on Graph Drawing, GD 2009, held in Chicago, USA, during September 2009. The 31 revised full papers and 4 short papers presented were carefully reviewed and selected out of 79 submissions. Furthermore, 10 posters were accepted in a separate submission process.

The Genome of Homo Sapiens

The Genome of Homo Sapiens Book
Author : David Stewart,Bruce Stillman
Publisher : CSHL Press
Release : 2003
ISBN : 9780879697105
Language : En, Es, Fr & De

GET BOOK

Book Description :

The Human Genome Project was completed in 2003, 50 years after the discovery of the structure of DNA and 17 years after an influential debate at the annual Cold Spring Harbor Laboratory Symposium about the Project's feasibility. The 2003 Symposium was dedicated to examining what has been learned so far from the human genome sequence. This book contains over sixty contributions from the world's leaders in this field and covers genome structure and evolution, methods of data analysis, lessons from species comparison, and the application of sequence data to the understanding of disease.

Literature based Discovery

Literature based Discovery Book
Author : Peter Bruza,Marc Weeber
Publisher : Springer Science & Business Media
Release : 2008-08-17
ISBN : 3540686908
Language : En, Es, Fr & De

GET BOOK

Book Description :

This is the first coherent book on literature-based discovery (LBD). LBD is an inherently multi-disciplinary enterprise. The aim of this volume is to plant a flag in the ground and inspire new researchers to the LBD challenge.

Gene therapy

Gene therapy Book
Author : Surendra Nimesh
Publisher : Elsevier
Release : 2013-10-31
ISBN : 1908818646
Language : En, Es, Fr & De

GET BOOK

Book Description :

Gene therapy is emerging as a new class of therapeutics for the treatment of inherited and acquired diseases. However, poor cellular uptake and instability of DNA in the physiological milieu limits its therapeutic potential, hence a vector which can protect and efficiently transport DNA to the target cells must be developed. Nanotechnology-based non-viral vectors have been proposed as potential candidates. Various polymeric nanoparticles have been shown to be suitable, with high cellular uptake efficiencies and reduced cytotoxicity. These delivery vectors form condensed complexes with DNA which result in shielding against enzymatic degradation and enhanced cellular targeting. Advantages including easy manipulatibility, high stability, low cost and high payload, mean that nanoparticles from various polymers have been exploited. Gene therapy gives a systematic account of the many aspects of nanotechnology mediated gene therapy, from the preparation of nanoparticles to physicochemical characterization, and follows with applications in in vitro and in vivo models. This book emphasizes the various aspects of nanotechnology-based gene therapy, with initial chapters detailing the tools and techniques available for preparation and in vitro and in vivo characterization of nanoparticles. Later chapters provide exhaustive details on polymeric systems employed for gene therapy. Provides an overview of nanotechnology applications in gene therapy, from preparation of nanoparticles to in vitro and in vivo studies Details the tools and techniques available for preparation, characterization and in vitro and in vivo study of nanoparticles Details the limitations of nanoparticle-mediated gene therapy and proposes ways in which they may be overcome

Biodata Mining And Visualization Novel Approaches

Biodata Mining And Visualization  Novel Approaches Book
Author : Havukkala Ilkka
Publisher : World Scientific Publishing Company
Release : 2010-06-23
ISBN : 9813107081
Language : En, Es, Fr & De

GET BOOK

Book Description :

There is a lack of an exposition on interdisciplinary and innovative methods of data mining and visualization for biodata. This book fills the gap by introducing an interdisciplinary set of the most recent methods and references on novel techniques from artificial intelligence, data mining, engineering, pattern recognition, and ontological data mining fields that are applicable to bioinformatics. The latest novel approaches are explained in detail, their advantages and disadvantages are summarized, and pointers to the future development of new applications are given. By widening the pool from which biologists and bioinformaticians can adopt methods for biodata mining and visualization, computational data mining experts in nonbiological fields are also encouraged to utilize their expertise in order to contribute to the progress of computational biology, thus enhancing the collaboration between these two disciplines.

Genome Annotation and Finding Repetitive DNA Elements

Genome Annotation and Finding Repetitive DNA Elements Book
Author : Renu Rawat
Publisher : Unknown
Release : 2014-06-03
ISBN : 9783656659815
Language : En, Es, Fr & De

GET BOOK

Book Description :

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

Summary Life Itself Francis Crick Annotated Study Aid by Scott Campbell

Summary  Life Itself  Francis Crick  Annotated Study Aid by Scott Campbell  Book
Author : Scott Campbell
Publisher : Scott Campbell
Release : 2021-12-08
ISBN : 0987650XXX
Language : En, Es, Fr & De

GET BOOK

Book Description :

Warning! Rather than the original text, this book summarizes the orginal text and also offers an annotation study aid--a form of efficiency that capitalizes on Crick's topics. It is not meant to replace Crick's popular and mind-blowing book. Having a good look at these topics may forever change your understanding of life on Earth.I selected Francis Crick’s Life Itself to update, summarize, and expand because he promoted the idea that DNA did not first evolve on Earth. If true, DNA’s alien origin would be one of the most important realizations in all Human history. Life, according to Crick, began somewhere else where conditions were more favorable and, with the help of advanced intelligence, seeded Earth through panspermic, “seeds everywhere,” events. This has been labeled as the “seeded hypothesis.” If DNA originated elsewhere, it reflects not only upon our beginnings as a form of “alien” or “alien hybrid” but also our future, which may include merging with one or more advanced civilizations. We may, indeed, one day, meet our “makers,” or at least some of their descendants. This ebook summarizes Crick’s work which previously could only be found, to the best of my knowledge, in printed form, adds the evidence of signatures and hidden mathematical and pictorial codes from DNA for his theory, offers general updates on cosmological data that Crick did not have at his disposal, addresses the subject of the surprising Last Universal Common Ancestor for life, and briefly explores our government’s about-face on the subject of Unidentified Aerial Phenomenon (UAP) and bizarre materials found at their landings which they admit having and examining.

Advances in Cyanobacterial Biology

Advances in Cyanobacterial Biology Book
Author : Prashant Kumar Singh,Ajay Kumar,Vipin Kumar Singh,Alok Kumar Shrivistava
Publisher : Academic Press
Release : 2020-02-15
ISBN : 0128193123
Language : En, Es, Fr & De

GET BOOK

Book Description :

Advances in Cyanobacterial Biology presents the novel, practical, and theoretical aspects of cyanobacteria, providing a better understanding of basic and advanced biotechnological application in the field of sustainable agriculture. Chapters have been designed to deal with the different aspects of cyanobacteria including their role in the evolution of life, cyanobacterial diversity and classification, isolation, and characterization of cyanobacteria through biochemical and molecular approaches, phylogeny and biogeography of cyanobacteria, symbiosis, Cyanobacterial photosynthesis, morphological and physiological adaptation to abiotic stresses, stress-tolerant cyanobacterium, biological nitrogen fixation. Other topics include circadian rhythms, genetics and molecular biology of abiotic stress responses, application of cyanobacteria and cyanobacterial mats in wastewater treatments, use as a source of novel stress-responsive genes for development of stress tolerance and as a source of biofuels, industrial application, as biofertilizer, cyanobacterial blooms, use in Nano-technology and nanomedicines as well as potential applications. This book will be important for academics and researchers working in cyanobacteria, cyanobacterial environmental biology, cyanobacterial agriculture and cyanobacterial molecular biologists. Summarizes the various aspects of cyanobacterial research, from primary nitrogen fixation, to advanced nano-technology applications Addresses both practical and theoretical aspects of the cyanobacterial application Includes coverage of biochemical and molecular approaches for the identification, use and management of cyanobacteria

Animal Science Reviews 2011

Animal Science Reviews 2011 Book
Author : David Hemming
Publisher : CABI
Release : 2012-01-01
ISBN : 9781780640181
Language : En, Es, Fr & De

GET BOOK

Book Description :

& Quot;Animal Science Reviews 2011" provides scientists and students in animal science with timely analysis on key topics in current research. Originally published online in CAB Reviews, this volume makes available in printed form the reviews in animal science published during 2011.

Comparative Annotation Toolkit CAT Simultaneous Clade and Personal Genome Annotation

Comparative Annotation Toolkit  CAT    Simultaneous Clade and Personal Genome Annotation Book
Author : Ian Fiddes
Publisher : Unknown
Release : 2017
ISBN : 9780355671698
Language : En, Es, Fr & De

GET BOOK

Book Description :

The recent introductions of low-cost, long-read and read-cloud sequencing technologies coupled with intense efforts to develop efficient algorithms have made affordable, high-quality de-novo sequence assembly a realistic proposition. The result is an explosion of new, ultra contiguous genome assemblies. To compare these genomes we need robust methods for genome annotation. I describe the fully open source Comparative Annotation Toolkit (CAT), which provides a flexible way to simultaneously annotate entire clades and identify orthology relationships. I show that CAT can be used to improve annotations on the rat genome, annotate the great apes, annotate a diverse set of mammals, and annotate personal, diploid human genomes. I demonstrate the resulting discovery of novel genes, isoforms and structural variants, even in genomes as well studied as the rat and great apes, and how these annotations improve cross-species RNA expression experiments.

Genome Research

Genome Research Book
Author : Anonim
Publisher : Unknown
Release : 2009
ISBN : 0987650XXX
Language : En, Es, Fr & De

GET BOOK

Book Description :

Download Genome Research book written by , available in PDF, EPUB, and Kindle, or read full book online anywhere and anytime. Compatible with any devices.