On Gene Prediction By Cross Species Comparative Sequence Analysis
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On Gene Prediction By Cross Species Comparative Sequence Analysis
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Author : Rong Chen
language : en
Publisher:
Release Date : 2003
On Gene Prediction By Cross Species Comparative Sequence Analysis written by Rong Chen and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2003 with Dynamic programming categories.
Gene Prediction By Combining Outputs From Exonhunter And Sgp2
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Author : Yujing Kuai
language : en
Publisher:
Release Date : 2009
Gene Prediction By Combining Outputs From Exonhunter And Sgp2 written by Yujing Kuai and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009 with categories.
Comparative Gene Finding
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Author : Marina Axelson-Fisk
language : en
Publisher: Springer
Release Date : 2015-04-13
Comparative Gene Finding written by Marina Axelson-Fisk and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-04-13 with Computers categories.
This book presents a guide to building computational gene finders, and describes the state of the art in computational gene finding methods, with a focus on comparative approaches. Fully updated and expanded, this new edition examines next-generation sequencing (NGS) technology. The book also discusses conditional random fields, enhancing the broad coverage of topics spanning probability theory, statistics, information theory, optimization theory and numerical analysis. Features: introduces the fundamental terms and concepts in the field; discusses algorithms for single-species gene finding, and approaches to pairwise and multiple sequence alignments, then describes how the strengths in both areas can be combined to improve the accuracy of gene finding; explores the gene features most commonly captured by a computational gene model, and explains the basics of parameter training; illustrates how to implement a comparative gene finder; examines NGS techniques and how to build a genome annotation pipeline.
Sequence Evolution Function
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Author : Eugene V. Koonin
language : en
Publisher: Springer Science & Business Media
Release Date : 2013-06-29
Sequence Evolution Function written by Eugene V. Koonin 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 2013-06-29 with Science categories.
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.
Comparative Gene Expression Analysis In Emiliania Huxleyi Isochrysis Galbana And Gephyrocapsa Oceanica
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Author : Arun Gopinath
language : en
Publisher:
Release Date : 2015
Comparative Gene Expression Analysis In Emiliania Huxleyi Isochrysis Galbana And Gephyrocapsa Oceanica written by Arun Gopinath and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015 with categories.
Comparative genomics is a field of biological research in which the genomic sequences of different species are compared. Comparative genomics provides a powerful tool for studying evolutionary changes among organisms, helping to identify genes that are conserved among species, as well as genes that give each organism its unique characteristics. Genome annotations of newly sequenced species initially rely primarily on ab initio gene predictions and alignment of reference transcripts of related species; however, the quality of gene models is greatly improved when incorporating same species transcriptomes. In this study, we started with the re-annotation of the E. huxleyi, G. oceanica and I. galbana based on de novo assembly of transcriptomes. De novo assembly tool TRINITY was used to assemble the transcriptomes of each individual sister species, followed by a pipeline based on Program to Assemble Spliced Alignments (PASA), ab initio gene predictors AUGUSTUS and SNAP, EvidenceModeler (EVM) and MAKER2. The pipeline was validated by re-annotating E. huxleyi, as we have a good first generation JGI E. huxleyi annotation. The revised E. huxleyi annotation describes 35,582 genes compared to 30,499 for first generation annotation. More than 95% of the previously annotated E.huxleyi genes mapped on to the re-annotated 35,582 E.huxleyi genes. The re-annotation pipeline predicted G.oceanica 52,680 genes compared to 28,441 for the previous annotation pipeline. Revised I.galbana annotation has 18,712 genes compared to 13,148 genes for the previous annotation. Once we re-annotated the sister species genome, we focused the research to comparative study. Various PASA, EVM and BLAST tools were used to determine the genome size, number of genes predicted, and number of shared genes among the sister species. The revised E. huxleyi annotation shares 31,734 orthologous genes with G. oceanica and 23,392 orthologous genes with I. galbana. Comparative study between G.oceanica and I.galbana found 15,358 common genes, with additional 20,800 G.oceanica genes sharing considerable similarity to the common G.oceanica-I.galbana genes. Further comparative study found 2,642 unique I.galbana genes; 3,137 unique E.huxleyi genes and 6,959 unique G.oceanica genes.
Biological Sequence Analysis
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Author : Richard Durbin
language : en
Publisher: Cambridge University Press
Release Date : 1998-04-23
Biological Sequence Analysis written by Richard Durbin and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 1998-04-23 with Science categories.
Presents up-to-date computer methods for analysing DNA, RNA and protein sequences.
Molecular Structure Of Nucleic Acids
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Author :
language : en
Publisher: Ardent Media
Release Date : 1953
Molecular Structure Of Nucleic Acids written by and has been published by Ardent Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 1953 with DNA. categories.
Computational Prediction Of Functional Elements Through Comparative Genomics
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Author : Xu Ling
language : en
Publisher:
Release Date : 2011-09-09
Computational Prediction Of Functional Elements Through Comparative Genomics written by Xu Ling and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011-09-09 with categories.
Understanding the evolution and organization of the genomic functional elements is one of the most important goals of genomic studies. The complexity of the functional information encoded in the genome sequences and the variabilities of the manners of encoding the information make it a very challenging task. Nucleotides mutations and genome-wide re-arrangements bring additional great challenges in identification and understanding of the functional elements in the genome. On the other hand, due to natural selection, functional sequences tend to evolve at a slower rate than non-functional sequences. Therefore, the conservation pattern across species often indicates where functional sequences are located. With the increasing number of species being sequenced, comparative genomes, which compares the sequences from multiple species at varying evolutionary distances, has now merged as a very powerful approach for identifying variety types of functional elements, such as protein coding genes, transcriptional regulatory sequences, and non-coding RNA genes. This dissertation research has been focused on two grand challenges of genomics: (i) to decode cis-regulatory modules (CRMs), non-coding DNA sequences controlling gene expression; and (ii) to discover gene groups that are functionally related. For both lines of work, the key idea is to leverage the power of comparative genomics in decoding the genomic information. The first part of this thesis developed a probabilistic framework for CRM prediction. This framework is based on a probabilistic model of CRM evolution, which captures the content feature of regulatory sequences as well as their dynamic process of evolution. This model advances the previous models by dealing with the inherent uncertainties of transcription factor binding site (TFBS) annotations in a probabilistic framework, as partially conserved binding site has been recognized as an important aspect of regulatory sequence evolution we explicitly model the two stochastic process of loss of existing TFBSs and TFBS gain from background nucleotides, to leverage the power of comparative genomics for CRM prediction, while at the same time utilize the information of this lineage-specific pattern. The second part of this thesis focuses on discovering functionally related gene groups. Understanding how genes are organized in the genomes and what information is encoded in genomic contexts is one of the fundamental problems in genomics. During evolution, the gene order is generally not well conserved because of the rapid rearrangement events that reshuffle genomes. On the other hand, functionally related genes may be constrained to remain close to each other due to natural selection, forming so called conserved gene clusters. Conservation of spatial organization of genes provides an important source of information that is orthogonal to primary sequences of genes and thus could be exploited to supplement our existing genomic analysis tools. In this thesis, we developed a highly efficient algorithm to discover conserved gene clusters across multiple genomes. These gene clusters are likely under some evolutionary constraint and indicate functional relationship among the genes within a cluster. Our algorithm advances existing work by allowing genes in the clusters to appear in different orders and at the same time making the computation orders of magnitude faster. This allows us to detect conserved gene clusters under flexible evolutionary constraints in a large number of genomes. In addition, we developed a statistical evaluation method, which incorporates the evolutionary relationship among genomes, a key aspect that has been missing in...
Pan Genomics Applications Challenges And Future Prospects
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Author : Debmalya Barh
language : en
Publisher: Academic Press
Release Date : 2020-03-06
Pan Genomics Applications Challenges And Future Prospects written by Debmalya Barh and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-03-06 with Science categories.
Pan-genomics: Applications, Challenges, and Future Prospects covers current approaches, challenges and future prospects of pan-genomics. The book discusses bioinformatics tools and their applications and focuses on bacterial comparative genomics in order to leverage the development of precise drugs and treatments for specific organisms. The book is divided into three sections: the first, an "overview of pan-genomics and common approaches, brings the main concepts and current approaches on pan-genomics research; the second, “case studies in pan-genomics, thoroughly discusses twelve case, and the last, “current approaches and future prospects in pan-multiomics , encompasses the developments on omics studies to be applied on bacteria related studies. This book is a valuable source for bioinformaticians, genomics researchers and several members of biomedical field interested in understanding further bacterial organisms and their relationship to human health. Covers the entire spectrum of pangenomics, highlighting the use of specific approaches, case studies and future perspectives Discusses current bioinformatics tools and strategies for exploiting pangenomics data Presents twelve case studies with different organisms in order to provide the audience with real examples of pangenomics applicability
The Yeast Two Hybrid System
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Author : Paul L. Bartel
language : en
Publisher: Oxford University Press, USA
Release Date : 1997
The Yeast Two Hybrid System written by Paul L. Bartel and has been published by Oxford University Press, USA this book supported file pdf, txt, epub, kindle and other format this book has been release on 1997 with Carrier proteins categories.
This volume, part of the Advances in Molecular Biology series, presents work by pioneers in the field and is the first publication devoted solely to the yeast two-hybrid system. It includes detailed protocols, practical advice on troubleshooting, and suggestions for future development. In addition, it illustrates how to construct an activation domain hybrid library, how to identify mutations that disrupt an interaction, and how to use the system in mammalian cells. Many of the contributors have developed new applications and variations of the technique.