Annotating New Genes

Annotating New Genes
Author: Shizuka Uchida
Publsiher: Elsevier
Total Pages: 196
Release: 2012-08-06
ISBN 10: 1908818123
ISBN 13: 9781908818126
Language: EN, FR, DE, ES & NL

Annotating New Genes Book Review:

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

Genome Annotation

Genome Annotation
Author: Jung Soh,Paul M.K. Gordon,Christoph W. Sensen
Publsiher: CRC Press
Total Pages: 270
Release: 2016-04-19
ISBN 10: 1439841187
ISBN 13: 9781439841181
Language: EN, FR, DE, ES & NL

Genome Annotation Book Review:

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.

Bioinformatics and Functional Genomics

Bioinformatics and Functional Genomics
Author: Jonathan Pevsner
Publsiher: John Wiley & Sons
Total Pages: 792
Release: 2005-03-04
ISBN 10: 0471459178
ISBN 13: 9780471459170
Language: EN, FR, DE, ES & NL

Bioinformatics and Functional Genomics Book Review:

Wiley is proud to announce the publication of the first ever broad-based textbook introduction to Bioinformatics and Functional Genomics by a trained biologist, experienced researcher, and award-winning instructor. In this new text, author Jonathan Pevsner, winner of the 2001 Johns Hopkins University "Teacher of the Year" award, explains problem-solving using bioinformatic approaches using real examples such as breast cancer, HIV-1, and retinal-binding protein throughout. His book includes 375 figures and over 170 tables. Each chapter includes: Problems, discussion of Pitfalls, Boxes explaining key techniques and math/stats principles, Summary, Recommended Reading list, and URLs for freely available software. The text is suitable for professionals and students at every level, including those with little to no background in computer science.

Development of New Tools and Pipelines for Plant Bioinformatics Applications

Development of New Tools and Pipelines for Plant Bioinformatics Applications
Author: Omar M. Darwish
Publsiher: Unknown
Total Pages: 140
Release: 2014
ISBN 10: 1928374650XXX
ISBN 13: OCLC:886514524
Language: EN, FR, DE, ES & NL

Development of New Tools and Pipelines for Plant Bioinformatics Applications Book Review:

Blueberry is an economically and nutritionally important small fruit crop, native to North America. As with many crops, extreme low temperature can affect blueberry crop yield negatively and cause major losses to growers. For this reason, blueberry breeding programs have focused on developing improved cultivars with broader climatic adaptation. To help achieve this goal, the blueberry genomic database (BBGD454) was developed to provide the research community with valuable resources to identify genes that play an important role in flower bud and fruit development, cold acclimation and chilling accumulation in blueberry. The database was developed using SQLServer2008 to house 454 transcript sequences, annotations and gene expression profiles of blueberry genes. BBGD454 can be accessed publically from a web-based interface; this website provides search and browse functionalities to allow scientists to access and search the data in order to correlate gene expression with gene function in different stages of blueberry fruit ripening, at different stages of cold acclimation of flower buds, and in leaves. It can be accessed from: http://bioinformatics.towson.edu/BBGD454. Fragaria vesca, a diploid strawberry species commonly known as the alpine or woodland strawberry, is a versatile experimental plant system and an emerging model for the Rosaceae family. An ancestral F. Vesca genome contributed to the genome of the octoploid dessert strawberry (F. × ananassa), and the extant genome exhibits synteny with other commercially important members of the Rosaceae family such as apple and peach. To provide a molecular description of floral organ and fruit development at the resolution of specific tissues and cell types, RNAs from flowers and early developmental stage fruit tissues of the inbred F. vesca line YW5AF7 were extracted and the resulting cDNA libraries sequenced using an Illumina HiSeq2000. To enable easy access as well as mining of this two-dimensional (stage and tissue) transcriptome dataset, a web-based database, the Strawberry Genomic Resource (SGR), was developed. SGR is a web accessible database that contains sample description, sample statistics, gene annotation, and gene expression analysis. This information can be accessed publicly from a web-based interface at http://bioinformatics.towson.edu/strawberry. The SGR website provides user friendly search and browse capabilities for all the data stored in the database. Users are able to search for genes using a gene ID or description or obtain differentially expressed genes by entering different comparison parameters. Search results can be downloaded in a tabular format compatible with Microsoft excel application. Aligned reads to individual genes and exon/intron structures are displayed using the genome browser, facilitating gene re-annotation by individual users. The SGR database was developed to facilitate dissemination and data mining of extensive floral and fruit transcriptome data in the woodland strawberry. It enables users to mine the data in different ways to study different pathways or biological processes during reproductive development. The F. vesca genome was sequenced in 2010. The current gene models (version 1.1) were developed using GeneMark-ES+, which did not use experimental evidence to partition the DNA sequence into coding and non-coding regions. Taking advantage of the extensive transcriptomic data of fifty different tissue/stage samples of early stage F. vesca fruit development, we re-annotated the F. vesca genome using the MAKER annotation pipeline. This re-annotation significantly improves the accuracy of gene structure and facilitates functional studies of individual strawberry genes. The new annotation described here identifies 33,496 protein-coding genes compared to 32,831 protein-coding genes in the old annotation hosted at the Genome Database of Rosaceae (GDR). The total coding length is 40,815,814 base pair in the new annotation compared to 38,750,535 base pair in the old annotation. Total number of coding regions in the proposed annotation is 176,409 compared to 167,270 in the GeneMark annotation. The total number of newly discovered gene models that were absent in previous annotations is 2286. Using extensive F. vesca RNA-Seq data, we re-annotated F. vesca genome. The number of protein-coding genes and the total coding length across all chromosomes are increased. This increase is due to the discovery of new genes, addition of exons to current genes, extension of current exons and merging of current exons. This complete genome re-annotation is hosted at SGR GBrowse and will significantly benefit the strawberry and Rosaceae research community as a whole.

Sequence Evolution Function

Sequence     Evolution     Function
Author: Eugene V. Koonin,Michael Galperin
Publsiher: Springer Science & Business Media
Total Pages: 462
Release: 2013-06-29
ISBN 10: 1475737831
ISBN 13: 9781475737837
Language: EN, FR, DE, ES & NL

Sequence Evolution Function Book Review:

Sequence - Evolution - Function is an introduction to the computational approaches that play a critical role in the emerging new branch of biology known as functional genomics. The book provides the reader with an understanding of the principles and approaches of functional genomics and of the potential and limitations of computational and experimental approaches to genome analysis. Sequence - Evolution - Function should help bridge the "digital divide" between biologists and computer scientists, allowing biologists to better grasp the peculiarities of the emerging field of Genome Biology and to learn how to benefit from the enormous amount of sequence data available in the public databases. The book is non-technical with respect to the computer methods for genome analysis and discusses these methods from the user's viewpoint, without addressing mathematical and algorithmic details. Prior practical familiarity with the basic methods for sequence analysis is a major advantage, but a reader without such experience will be able to use the book as an introduction to these methods. This book is perfect for introductory level courses in computational methods for comparative and functional genomics.

Gene Prediction

Gene Prediction
Author: Martin Kollmar
Publsiher: Humana Press
Total Pages: 284
Release: 2019-05-19
ISBN 10: 9781493991723
ISBN 13: 1493991728
Language: EN, FR, DE, ES & NL

Gene Prediction Book Review:

This volume introduces software used for gene prediction with focus on eukaryotic genomes. The chapters in this book describe software and web server usage as applied in common use-cases, and explain ways to simplify re-annotation of long available genome assemblies. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary computational requirements, step-by-step, readily reproducible computational protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, Gene Prediction: Methods and Protocols is a valuable resource for researchers and research groups working on the assembly and annotation of single species or small groups of species. Chapter 3 is available open access under a CC BY 4.0 license via link.springer.com.

IMG ER

IMG ER
Author: Anonim
Publsiher: Unknown
Total Pages: 135
Release: 2009
ISBN 10: 1928374650XXX
ISBN 13: OCLC:727280523
Language: EN, FR, DE, ES & NL

IMG ER Book Review:

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.

Encyclopedia of Bioinformatics and Computational Biology

Encyclopedia of Bioinformatics and Computational Biology
Author: Anonim
Publsiher: Elsevier
Total Pages: 3284
Release: 2018-08-21
ISBN 10: 0128114320
ISBN 13: 9780128114322
Language: EN, FR, DE, ES & NL

Encyclopedia of Bioinformatics and Computational Biology Book Review:

Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics combines elements of computer science, information technology, mathematics, statistics and biotechnology, providing the methodology and in silico solutions to mine biological data and processes. The book covers Theory, Topics and Applications, with a special focus on Integrative –omics and Systems Biology. The theoretical, methodological underpinnings of BCB, including phylogeny are covered, as are more current areas of focus, such as translational bioinformatics, cheminformatics, and environmental informatics. Finally, Applications provide guidance for commonly asked questions. This major reference work spans basic and cutting-edge methodologies authored by leaders in the field, providing an invaluable resource for students, scientists, professionals in research institutes, and a broad swath of researchers in biotechnology and the biomedical and pharmaceutical industries. Brings together information from computer science, information technology, mathematics, statistics and biotechnology Written and reviewed by leading experts in the field, providing a unique and authoritative resource Focuses on the main theoretical and methodological concepts before expanding on specific topics and applications Includes interactive images, multimedia tools and crosslinking to further resources and databases

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
Author: Matthew Morritt Hindle
Publsiher: Unknown
Total Pages: 135
Release: 2012
ISBN 10: 1928374650XXX
ISBN 13: OCLC:824173959
Language: EN, FR, DE, ES & NL

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

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.

The Gene Ontology Handbook

The Gene Ontology Handbook
Author: Christophe Dessimoz,Nives Skunca
Publsiher: Unknown
Total Pages: 298
Release: 2020-10-08
ISBN 10: 9781013267703
ISBN 13: 1013267702
Language: EN, FR, DE, ES & NL

The Gene Ontology Handbook Book Review:

This book provides a practical and self-contained overview of the Gene Ontology (GO), the leading project to organize biological knowledge on genes and their products across genomic resources. Written for biologists and bioinformaticians, it covers the state-of-the-art of how GO annotations are made, how they are evaluated, and what sort of analyses can and cannot be done with the GO. In the spirit of the Methods in Molecular Biology book series, there is an emphasis throughout the chapters on providing practical guidance and troubleshooting advice. Authoritative and accessible, The Gene Ontology Handbook serves non-experts as well as seasoned GO users as a thorough guide to this powerful knowledge system. This work was published by Saint Philip Street Press pursuant to a Creative Commons license permitting commercial use. All rights not granted by the work's license are retained by the author or authors.

Modern Genome Annotation

Modern Genome Annotation
Author: D. Frishman,Alfonso Valencia
Publsiher: Springer Science & Business Media
Total Pages: 490
Release: 2009-10-02
ISBN 10: 3211751238
ISBN 13: 9783211751237
Language: EN, FR, DE, ES & NL

Modern Genome Annotation Book Review:

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.

Computational Genomics with R

Computational Genomics with R
Author: Altuna Akalin
Publsiher: Chapman & Hall/CRC Computational Biology Series
Total Pages: 462
Release: 2020-11-26
ISBN 10: 9781498781855
ISBN 13: 1498781853
Language: EN, FR, DE, ES & NL

Computational Genomics with R Book Review:

Computational Genomics with R provides a starting point for beginners in genomic data analysis and also guides more advanced practitioners to sophisticated data analysis techniques in genomics. The book covers topics from R programming, to machine learning and statistics, to the latest genomic data analysis techniques. The text provides accessible information and explanations, always with the genomics context in the background. This also contains practical and well-documented examples in R so readers can analyze their data by simply reusing the code presented. As the field of computational genomics is interdisciplinary, it requires different starting points for people with different backgrounds. For example, a biologist might skip sections on basic genome biology and start with R programming, whereas a computer scientist might want to start with genome biology. After reading: You will have the basics of R and be able to dive right into specialized uses of R for computational genomics such as using Bioconductor packages. You will be familiar with statistics, supervised and unsupervised learning techniques that are important in data modeling, and exploratory analysis of high-dimensional data. You will understand genomic intervals and operations on them that are used for tasks such as aligned read counting and genomic feature annotation. You will know the basics of processing and quality checking high-throughput sequencing data. You will be able to do sequence analysis, such as calculating GC content for parts of a genome or finding transcription factor binding sites. You will know about visualization techniques used in genomics, such as heatmaps, meta-gene plots, and genomic track visualization. You will be familiar with analysis of different high-throughput sequencing data sets, such as RNA-seq, ChIP-seq, and BS-seq. You will know basic techniques for integrating and interpreting multi-omics datasets. Altuna Akalin is a group leader and head of the Bioinformatics and Omics Data Science Platform at the Berlin Institute of Medical Systems Biology, Max Delbrück Center, Berlin. He has been developing computational methods for analyzing and integrating large-scale genomics data sets since 2002. He has published an extensive body of work in this area. The framework for this book grew out of the yearly computational genomics courses he has been organizing and teaching since 2015.

Next Generation Sequencing

Next Generation Sequencing
Author: Jerzy Kulski
Publsiher: BoD – Books on Demand
Total Pages: 464
Release: 2016-01-14
ISBN 10: 9535122401
ISBN 13: 9789535122401
Language: EN, FR, DE, ES & NL

Next Generation Sequencing Book Review:

Next generation sequencing (NGS) has surpassed the traditional Sanger sequencing method to become the main choice for large-scale, genome-wide sequencing studies with ultra-high-throughput production and a huge reduction in costs. The NGS technologies have had enormous impact on the studies of structural and functional genomics in all the life sciences. In this book, Next Generation Sequencing Advances, Applications and Challenges, the sixteen chapters written by experts cover various aspects of NGS including genomics, transcriptomics and methylomics, the sequencing platforms, and the bioinformatics challenges in processing and analysing huge amounts of sequencing data. Following an overview of the evolution of NGS in the brave new world of omics, the book examines the advances and challenges of NGS applications in basic and applied research on microorganisms, agricultural plants and humans. This book is of value to all who are interested in DNA sequencing and bioinformatics across all fields of the life sciences.

Bioinformatics in Aquaculture

Bioinformatics in Aquaculture
Author: Zhanjiang (John) Liu
Publsiher: John Wiley & Sons
Total Pages: 606
Release: 2017-04-17
ISBN 10: 1118782356
ISBN 13: 9781118782354
Language: EN, FR, DE, ES & NL

Bioinformatics in Aquaculture Book Review:

Bioinformatics derives knowledge from computer analysis of biological data. In particular, genomic and transcriptomic datasets are processed, analysed and, whenever possible, associated with experimental results from various sources, to draw structural, organizational, and functional information relevant to biology. Research in bioinformatics includes method development for storage, retrieval, and analysis of the data. Bioinformatics in Aquaculture provides the most up to date reviews of next generation sequencing technologies, their applications in aquaculture, and principles and methodologies for the analysis of genomic and transcriptomic large datasets using bioinformatic methods, algorithm, and databases. The book is unique in providing guidance for the best software packages suitable for various analysis, providing detailed examples of using bioinformatic software and command lines in the context of real world experiments. This book is a vital tool for all those working in genomics, molecular biology, biochemistry and genetics related to aquaculture, and computational and biological sciences.

Database Annotation in Molecular Biology

Database Annotation in Molecular Biology
Author: Arthur M. Lesk
Publsiher: John Wiley & Sons
Total Pages: 266
Release: 2005-09-01
ISBN 10: 0470856858
ISBN 13: 9780470856857
Language: EN, FR, DE, ES & NL

Database Annotation in Molecular Biology Book Review:

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.

Gene Function

Gene Function
Author: S. Rosenthal,H. Bielka,Ch. Coutelle
Publsiher: Elsevier
Total Pages: 564
Release: 2014-05-09
ISBN 10: 1483188515
ISBN 13: 9781483188515
Language: EN, FR, DE, ES & NL

Gene Function Book Review:

Gene Function, contains the proceedings of the 12th Meeting of the Federation of European Biochemical Societies held in Dresden, Germany in 1978. The meeting provided a forum for discussing progress in the understanding of gene function and covered topics ranging from the functional organization of chromatin to principles of interactions and recognition models. The role of DNA sequence in the recognition of restriction endonucleases and modification enzymes is also examined, along with gene expression, RNA processing and modification, and isolation and synthesis of genes. Comprised of 49 chapters, this volume begins with an overview of what can be learned from the genetic analysis of the lac repressor, followed by a discussion on the topography of the interaction the lac repressor, RNA polymerase, and histones with DNA. The reader is then introduced to complementarity and recognition code between regulatory proteins and DNA; chromatin replication in vitro; and the cytoplasmic "petite" mutation in Saccharomyces cerevisiae. Subsequent chapters explore arc-like and helical arrangements of nucleosome cores; changes in gene expression during cellular differentiation; polyadenylation and processing of pre-messenger RNA; and the molecular biology of bacteriophages T3 and T7. This book will be of interest to geneticists, biochemists, and molecular biologists.

The Carrot Genome

The Carrot Genome
Author: Philipp Simon,Massimo Iorizzo,Dariusz Grzebelus,Rafal Baranski
Publsiher: Springer
Total Pages: 372
Release: 2019-05-08
ISBN 10: 3030033899
ISBN 13: 9783030033897
Language: EN, FR, DE, ES & NL

The Carrot Genome Book Review:

This book provides an up-to-date review and analysis of the carrot’s nuclear and organellar genome structure and evolution. In addition, it highlights applications of carrot genomic information to elucidate the carrot’s natural and agricultural history, reproductive biology, and the genetic basis of traits important in agriculture and human health. The carrot genome was sequenced in 2016, and its relatively small diploid genome, combined with the fact that it is the most complete root crop genome released to date and the first-ever Euasterid II genome to be sequenced, mean the carrot has an important role in the study of plant development and evolution. In addition, the carrot is among the top ten vegetables grown worldwide, and the abundant orange provitamin A carotenoids that account for its familiar orange color make it the richest crop source of vitamin A in the US diet, and in much of the world. This book includes the latest genetic maps, genetic tools and resources, and covers advances in genetic engineering that are relevant for plant breeders and biologists alike.

The Peanut Genome

The Peanut Genome
Author: Rajeev K. Varshney,Manish K. Pandey,Naveen Puppala
Publsiher: Springer
Total Pages: 169
Release: 2017-12-16
ISBN 10: 3319639358
ISBN 13: 9783319639352
Language: EN, FR, DE, ES & NL

The Peanut Genome Book Review:

This book presents the current state of the art in peanut genomics, focusing particularly on the latest genomic findings, tools and strategies employed in genome sequencing, transcriptomes and analysis, availability of public and private genomic resources, and ways to maximize the use of this information in peanut breeding programs. Further, it demonstrates how advances in plant genomics can be used to improve crop breeding. The peanut or groundnut (Arachis hypogaea L. Millsp) is a globally important grain legume and oilseed crop, cultivated in over 100 countries and consumed in the form of roasted seeds, oil and confectionary in nearly every country on Earth. The peanut contributes towards achieving food and nutritional security, in addition to financial security through income generation; as such, it is also vital to the livelihood of the poor in the developing world. There have been significant advances in peanut research, especially in the last five years, including sequencing the genome of both diploid progenitors, and the availability of tremendous transcriptome resources, large-scale genomic variations that can be used as genetic markers, genetic populations (bi- and multiparent populations and germplasm sets), marker-trait associations and molecular breeding products. The immediate availability of the genome sequence for tetraploid cultivated peanuts is the most essential genomic resource for achieving a deeper understanding of peanut traits and their use in breeding programs.

Transcription of Human specific Duplicate Genes

Transcription of Human specific Duplicate Genes
Author: Max L. Dougherty
Publsiher: Unknown
Total Pages: 162
Release: 2018
ISBN 10: 1928374650XXX
ISBN 13: OCLC:1080590018
Language: EN, FR, DE, ES & NL

Transcription of Human specific Duplicate Genes Book Review:

In this work, I set out to characterize new genes contained specifically within the human genome but absent from any other, including our closest evolutionary cousins. Our interest in these genes is twofold: First, gene duplication is a fundamental process by which evolutionary innovations at the organismal level arise; and second, we believe that variation in these new genes is an important and unappreciated source of phenotypic differences between individuals, both normal and pathogenic. The ability to interpret observed variation in a gene, such as to determine if a mutation in that gene is likely to be impactful, requires quality annotation. This includes an understanding of gene structure: how the gene is transcribed, processed, and which base pairs code for protein or have other specific roles. The major challenge presented by this category of genes is that they are highly identical to other parts of the genome, and as such, most methods of investigation struggle to tell them apart. As will be expanded upon, this annotation is currently absent or insufficient for genes that are specific to the human genome. Combined with evolutionary and expression analysis, solving this annotation problem enables us to understand how new genes are created in the human genome at the very earliest stages. Combined with surveys of natural occurring and pathogenic variation, it enables us to understand which new genes are functional and which are not, and among those with function, which harbor deleterious variants that can cause disease. With these goals in mind, I set out to solve the annotation of human-specific duplicate genes most promising for functional status. I performed a close study of one such gene, HYDIN2, where I present an evolutionary analysis that gives insight into gene creation and associated disease mechanism, present a survey of naturally occurring variation, and describe the complex transcriptional pattern of a gene that serves as a case study in how duplication and rearrangement of genome segments can lead to rapid gene innovation. Next, I present a technique to more rapidly and rigorously study the transcription of any recently created duplicate gene. I apply this technique to the body of human-specific duplicate genes as well as other expanded gene families. I show that by improving upon current annotations we gain insight into the structural history, expression pattern, and functional status of such genes. I conclude with logical next steps and promising future directions. Ultimately, this work increments our understanding of how gene duplication leads to evolutionary innovation specifically in human, the functional impact of these species-specific differences, and how variation in these genes can contribute to disease.

Bioinformatics

Bioinformatics
Author: Andreas D. Baxevanis,B. F. Francis Ouellette
Publsiher: John Wiley & Sons
Total Pages: 504
Release: 2004-03-24
ISBN 10: 0471461016
ISBN 13: 9780471461012
Language: EN, FR, DE, ES & NL

Bioinformatics Book Review:

"In this book, Andy Baxevanis and Francis Ouellette . . . haveundertaken the difficult task of organizing the knowledge in thisfield in a logical progression and presenting it in a digestibleform. And they have done an excellent job. This fine text will makea major impact on biological research and, in turn, on progress inbiomedicine. We are all in their debt." —Eric Lander from the Foreword Reviews from the First Edition "...provides a broad overview of the basic tools for sequenceanalysis ... For biologists approaching this subject for the firsttime, it will be a very useful handbook to keep on the shelf afterthe first reading, close to the computer." —Nature Structural Biology "...should be in the personal library of any biologist who usesthe Internet for the analysis of DNA and protein sequencedata." —Science "...a wonderful primer designed to navigate the novice throughthe intricacies of in scripto analysis ... The accomplished genesearcher will also find this book a useful addition to theirlibrary ... an excellent reference to the principles ofbioinformatics." —Trends in Biochemical Sciences This new edition of the highly successful Bioinformatics:A Practical Guide to the Analysis of Genes and Proteinsprovides a sound foundation of basic concepts, with practicaldiscussions and comparisons of both computational tools anddatabases relevant to biological research. Equipping biologists with the modern tools necessary to solvepractical problems in sequence data analysis, the Second Editioncovers the broad spectrum of topics in bioinformatics, ranging fromInternet concepts to predictive algorithms used on sequence,structure, and expression data. With chapters written by experts inthe field, this up-to-date reference thoroughly covers vitalconcepts and is appropriate for both the novice and the experiencedpractitioner. Written in clear, simple language, the book isaccessible to users without an advanced mathematical or computerscience background. This new edition includes: All new end-of-chapter Web resources, bibliographies, andproblem sets Accompanying Web site containing the answers to the problems,as well as links to relevant Web resources New coverage of comparative genomics, large-scale genomeanalysis, sequence assembly, and expressed sequence tags A glossary of commonly used terms in bioinformatics andgenomics Bioinformatics: A Practical Guide to the Analysis of Genesand Proteins, Second Edition is essential reading forresearchers, instructors, and students of all levels in molecularbiology and bioinformatics, as well as for investigators involvedin genomics, positional cloning, clinical research, andcomputational biology.