Problems and Solutions in Biological Sequence Analysis

Problems and Solutions in Biological Sequence Analysis

Building. phylogenetic. trees. The discussion of the concept of pairwise sequence
alignment and algorithms for finding optimal alignments was divided in BSA into
two chapters (Chapters 2 and 3). Chapter2 ...

Author: Mark Borodovsky

Publisher: Cambridge University Press

ISBN: 9781139458122

Category: Science

Page:

View: 708

This book is the first of its kind to provide a large collection of bioinformatics problems with accompanying solutions. Notably, the problem set includes all of the problems offered in Biological Sequence Analysis (BSA), by Durbin et al., widely adopted as a required text for bioinformatics courses at leading universities worldwide. Although many of the problems included in BSA as exercises for its readers have been repeatedly used for homework and tests, no detailed solutions for the problems were available. Bioinformatics instructors had therefore frequently expressed a need for fully worked solutions and a larger set of problems for use on courses. This book provides just that: following the same structure as BSA and significantly extending the set of workable problems, it will facilitate a better understanding of the contents of the chapters in BSA and will help its readers develop problem-solving skills that are vitally important for conducting successful research in the growing field of bioinformatics. All of the material has been class-tested by the authors at Georgia Tech, where the first ever M.Sc. degree program in Bioinformatics was held.
Categories: Science

Phylogenetics

Phylogenetics

The long-awaited revision of the industry standard on phylogenetics Since the publication of the first edition of this landmark volume more than twenty-five years ago, phylogenetic systematics has taken its place as the dominant paradigm of ...

Author: E. O. Wiley

Publisher: John Wiley & Sons

ISBN: 9781118017876

Category: Science

Page: 424

View: 869

The long-awaited revision of the industry standard on phylogenetics Since the publication of the first edition of this landmark volume more than twenty-five years ago, phylogenetic systematics has taken its place as the dominant paradigm of systematic biology. It has profoundly influenced the way scientists study evolution, and has seen many theoretical and technical advances as the field has continued to grow. It goes almost without saying that the next twenty-five years of phylogenetic research will prove as fascinating as the first, with many exciting developments yet to come. This new edition of Phylogenetics captures the very essence of this rapidly evolving discipline. Written for the practicing systematist and phylogeneticist, it addresses both the philosophical and technical issues of the field, as well as surveys general practices in taxonomy. Major sections of the book deal with the nature of species and higher taxa, homology and characters, trees and tree graphs, and biogeography—the purpose being to develop biologically relevant species, character, tree, and biogeographic concepts that can be applied fruitfully to phylogenetics. The book then turns its focus to phylogenetic trees, including an in-depth guide to tree-building algorithms. Additional coverage includes: Parsimony and parsimony analysis Parametric phylogenetics including maximum likelihood and Bayesian approaches Phylogenetic classification Critiques of evolutionary taxonomy, phenetics, and transformed cladistics Specimen selection, field collecting, and curating Systematic publication and the rules of nomenclature Providing a thorough synthesis of the field, this important update to Phylogenetics is essential for students and researchers in the areas of evolutionary biology, molecular evolution, genetics and evolutionary genetics, paleontology, physical anthropology, and zoology.
Categories: Science

The Great Tree of Life

The Great Tree of Life

By the 1980s and 1990s, tree-building had become a full-fledged science! Yet,
assembling an actual tree of all named life remained unfathomable—a
biodiversity moonshot. READING PHYLOGENETIC TREES Learning how to read
and to ...

Author: Douglas Soltis

Publisher: Academic Press

ISBN: 9780128125595

Category: Science

Page: 184

View: 535

The Great Tree of Life is a concise, approachable treatment that surveys the concept of the Tree of Life, including chapters on its historical introduction and cultural connection. The Tree of Life is a metaphor used to describe the relationships between organisms, both living and extinct. It has been widely recognized that the relationship between the roughly 10 million species on earth drives the ecological system. This work covers options on how to build the tree, demonstrating its utility in drug discovery, curing disease, crop improvement, conservation biology and ecology, along with tactics on how to respond to the challenges of climate change. This book is a key aid on the improvement of our understanding of the relationships between species, the increasing and essential awareness of biodiversity, and the power of employing modern biology to build the tree of life. Provides a single reference describing the properties, history and utility of The Tree of Life Introduces phylogenetics and its applications in an approachable manner Written by experts on the Tree of Life Includes an online companion site containing various original videos to enhance the reader’s understanding and experience
Categories: Science

Evolutionary Biology Mechanisms and Trends

Evolutionary Biology  Mechanisms and Trends

It is, however, necessary to extend this method for large number of molecular
traits in order to achieve a polygenic consensus representation of phylogeny. The
most important objective of constructing phylogenetic trees based on multiple ...

Author: Pierre Pontarotti

Publisher: Springer Science & Business Media

ISBN: 9783642304255

Category: Science

Page: 364

View: 400

The annual Evolutionary Biology Meetings in Marseilles serve to gather leading evolutionary biologists and other scientists using evolutionary biology concepts, e.g. for medical research. The aims of these meetings are to promote the exchange of ideas and to encourage interdisciplinary collaborations. This book collects 19 selected contributions presented at the 15th meeting, which took place in September 2011. It starts with a description of the life and work of J.B.S. Haldane, a remarkable evolutionary biologist of the 20th century. The remaining chapters are grouped under the following three themes: · New Concepts in Evolutionary Biology · Macroevolution: Mechanisms and Trends · Genome Evolution Offering an up-to-date overview of recent results in the field of evolutionary biology, this book is an invaluable source of information for scientists, teachers and advanced students.
Categories: Science

Astrobiology

Astrobiology

8.10. Complications. in. Building. Trees. This chapter so far has given the
impression that by comparing characteristics of organisms, such as their DNA,
and quantifying the differences, we can construct a phylogenetic tree. This is
broadly true.

Author: Charles S. Cockell

Publisher: John Wiley & Sons

ISBN: 9781119550396

Category: Science

Page: 632

View: 142

A guide to understanding the formation of life in the Universe The revised and updated second edition of Astrobiology offers an introductory text that explores the structure of living things, the formation of the elements required for life in the Universe, the biological and geological history of the Earth, and the habitability of other planets. Written by a noted expert on the topic, the book examines many of the major conceptual foundations in astrobiology, which cover a diversity of traditional fields including chemistry, biology, geosciences, physics, and astronomy. The book explores many profound questions such as: How did life originate on Earth? How has life persisted on Earth for over three billion years? Is there life elsewhere in the Universe? What is the future of life on Earth? Astrobiology is centered on investigating the past and future of life on Earth by looking beyond Earth to get the answers. Astrobiology links the diverse scientific fields needed to understand life on our own planet and, potentially, life beyond. This new second edition: Expands on information about the nature of astrobiology and why it is useful Contains a new chapter “What is Life?” that explores the history of attempts to understand life Contains 20% more material on the astrobiology of Mars, icy moons, the structure of life, and the habitability of planets New ‘Discussion Boxes’ to stimulate debate and thought about key questions in astrobiology New review and reflection questions for each chapter to aid learning New boxes describing the careers of astrobiologists and how they got into the subject Offers revised and updated information throughout to reflect the latest advances in the field Written for students of life sciences, physics, astronomy and related disciplines, the updated edition of Astrobiology is an essential introductory text that includes recent advances to this dynamic field.
Categories: Science

Combinatorial Algorithms for Constructing Phylogenetic Trees

Combinatorial Algorithms for Constructing Phylogenetic Trees

The class of k - trees has the following recursive definition : the complete graph
on k vertices is a k - tree : if G = ( V , E ) is a k ... This definition provides a way of
building up a h - tree beginning with a k - clique , and attaching new vertices to k
 ...

Author: Tandy Jo Warnow

Publisher:

ISBN: UCAL:C3366111

Category:

Page: 174

View: 644

Categories:

Molecular Evolution and Phylogenetics

Molecular Evolution and Phylogenetics

The text covers measurement of sequence divergence, construction of phylogenetic trees, statistical tests for detection of positive Darwinian selection, inference of ancestral amino acid sequences, construction of linearized trees, and ...

Author: Masatoshi Nei

Publisher: Oxford University Press

ISBN: 9780199881222

Category: Science

Page: 352

View: 884

During the last ten years, remarkable progress has occurred in the study of molecular evolution. Among the most important factors that are responsible for this progress are the development of new statistical methods and advances in computational technology. In particular, phylogenetic analysis of DNA or protein sequences has become a powerful tool for studying molecular evolution. Along with this developing technology, the application of the new statistical and computational methods has become more complicated and there is no comprehensive volume that treats these methods in depth. Molecular Evolution and Phylogenetics fills this gap and present various statistical methods that are easily accessible to general biologists as well as biochemists, bioinformatists and graduate students. The text covers measurement of sequence divergence, construction of phylogenetic trees, statistical tests for detection of positive Darwinian selection, inference of ancestral amino acid sequences, construction of linearized trees, and analysis of allele frequency data. Emphasis is given to practical methods of data analysis, and methods can be learned by working through numerical examples using the computer program MEGA2 that is provided.
Categories: Science

Phylogenetic Trees Made Easy

Phylogenetic Trees Made Easy

Chapter 2 will not lead to the optimal tree based on the data , so details of the
various steps are covered in later chapters . There are several distinct and
equally important steps that are involved in making a tree based upon molecular
 ...

Author: Barry G. Hall

Publisher: Sinauer Associates, Incorporated

ISBN: UCSD:31822034661165

Category: Computers

Page: 233

View: 770

Barry G. Hall helps beginners get started in creating phylogenetic trees from protein or nucleic acid sequence data.
Categories: Computers

Enhance the Understanding of Whole genome Evolution by Designing Accelerating and Parallelizing Phylogenetic Algorithms

Enhance the Understanding of Whole genome Evolution by Designing  Accelerating and Parallelizing Phylogenetic Algorithms

The advent of new technology enhance the speed and reduce the cost for sequencing biological data.

Author: Zhaoming Yin

Publisher:

ISBN: OCLC:890907197

Category: Algorithms

Page:

View: 144

The advent of new technology enhance the speed and reduce the cost for sequencing biological data. Making biological sense of this genomic data is a big challenge to the algorithm design as well as the high performance computing society. There are many problems in Bioinformatics, such as how new functional genes arise, why genes are organized into chromosomes, how species are connected through the evolutionary tree of life, or why arrangements are subject to change. Phylogenetic analyses have become essential to research on the evolutionary tree of life. It can help us to track the history of species and the relationship between different genes or genomes through millions of years. One of the fundamentals for phylogenetic construction is the computation of distances between genomes. Since there are much more complicated combinatoric patterns in rearrangement events, the distance computation is still a hot topic as much belongs to mathematics as to biology. For the distance computation with input of two genomes containing unequal gene contents (with insertions/deletions and duplications) the problem is especially hard. In this thesis, we will discuss about our contributions to the distance estimation for unequal gene order data. The problem of finding the median of three genomes is the key process in building the most parsimonious phylogenetic trees from genome rearrangement data. For genomes with unequal contents, to the best of our knowledge, there is no algorithm that can help to find the median. In this thesis, we make our contributions to the median computation in two aspects. 1) Algorithm engineering aspect, we harness the power of streaming graph analytics methods to implement an exact DCJ median algorithm which run as fast as the heuristic algorithm and can help construct a better phylogenetic tree. 2) Algorithmic aspect, we theoretically formulate the problem of finding median with input of genomes having unequal gene content, which leads to the design and implementation of an efficient Lin-Kernighan heuristic based median algorithm. Inferring phylogenies (evolutionary history) of a set of given species is the ultimate goal when the distance and median model are chosen. For more than a decade, biologists and computer scientists have studied how to infer phylogenies by the measurement of genome rearrangement events using gene order data. While evolution is not an inherently parsimonious process, maximum parsimony (MP) phylogenetic analysis has been supported by widely applied to the phylogeny inference to study the evolutionary patterns of genome rearrangements. There are generally two problems with the MP phylogenetic arose by genome rearrangement: One is, given a set of modern genomes, how to compute the topologies of the according phylogenetic tree; Another is, given the topology of a model tree, how to infer the gene orders of the ancestor species. To assemble a MP phylogenetic tree constructor, there are multiple NP hard problems involved, unfortunately, they organized as one problem on top of other problems. Which means, to solve a NP hard problem, we need to solve multiple NP hard sub-problems. For phylogenetic tree construction with the input of unequal content genomes, there are three layers of NP hard problems. In this thesis, we will mainly discuss about our contributions to the design and implementation of the software package DCJUC (Phylogeny Inference using DCJ model to cope with Unequal Content Genomes), that can help to achieve both of these two goals. Aside from the biological problems, another issue we need to concern is about the use of the power of parallel computing to assist accelerating algorithms to handle huge data sets, such as the high resolution gene order data. For one thing, all of the method to tackle with phylogenetic problems are based on branch and bound algorithms, which are quite irregular and unfriendly to parallel computing. To parallelize these algorithms, we need to properly enhance the efficiency for localized memory access and load balance methods to make sure that each thread can put their potentials into full play. For the other, there is a revolution taking place in computing with the availability of commodity graphical processors such as Nvidia GPU and with many-core CPUs such as Cray-XMT, or Intel Xeon Phi Coprocessor with 60 cores. These architectures provide a new way for us to achieve high performance at much lower cost. However, code running on these machines are not so easily programmed, and scientific computing is hard to tune well on them. We try to explore the potentials of these architectures to help us accelerate branch and bound based phylogenetic algorithms.
Categories: Algorithms

Encyclopedia of Genetics

Encyclopedia of Genetics

Unfortunately, however, many methods for building phylogenetic trees produce
unrooted trees, such as the tree shown in Figure I C. An unrooted tree can be
converted to a rooted tree if the position of the root is specified. Trees of Figures
1A ...

Author: Sydney Brenner

Publisher:

ISBN: STANFORD:36105025788782

Category: Science

Page: 2257

View: 194

Provides entries that cover all aspects of the field of genetics.
Categories: Science

The centrality of phylogenetic thinking

The centrality of phylogenetic thinking

Today , almost all systematists are phylogenetic systematists , also called cladists
. Broadly speaking , this simply means that systematists share a common goal
accomplished by building phylogenetic trees . A phylogenetic tree is a way of ...

Author: Matthew Horace Haber

Publisher:

ISBN: UCAL:X71000

Category:

Page: 222

View: 472

Categories:

Proceedings of the Twenty fifth Annual ACM Symposium on Theory of Computing

Proceedings of the Twenty fifth Annual ACM Symposium on Theory of Computing

Thus , we present perhaps the first algorithm for constructing phylogenetic trees
from distance matrices which finds optimal trees for a reasonable criterion in
polynomial time . 1 INTRODUCTION Constructing evolutionary trees for species
sets ...

Author:

Publisher: Assn for Computing Machinery

ISBN: 0897915917

Category: Computation theory

Page: 812

View: 553

Categories: Computation theory

Principles of Animal Behavior

Principles of Animal Behavior

Bird Bat Insect phylogenetic tree building . Ideally , we would like to be able to
build phylogenetic trees by including homologies , but eliminating homoplasies .
In practice , however , this is very difficult to do , as it is often hard to distinguish ...

Author: Lee Alan Dugatkin

Publisher: W W Norton & Company Incorporated

ISBN: STANFORD:36105131619780

Category: Science

Page: 642

View: 348

The most balanced, comprehensive and current animal behavior text available.
Categories: Science

DNA and Tissue Banking for Biodiversity and Conservation

DNA and Tissue Banking for Biodiversity and Conservation

Several methods are used for building phylogenetic trees , such as distance
matrix methods , maximum parsimony optimality criteria , likelihood calculations
and Bayesian statistics . Dozens of phylogenetic computer programs are
available ...

Author: Martyn P. Powell

Publisher: Royal Botanic Gardens Kew

ISBN: STANFORD:36105114545028

Category: Science

Page: 151

View: 597

DNA and Tissue Banking provides a practical and legislative framework covering uses of DNA, requirements of the Convention on Biological Diversity and CITES, model legal documents, practical guidelines for setting up DNA and tissue banks and worldwide case studies.
Categories: Science

The American Biology Teacher

The American Biology Teacher

Nevertheless , we know that “ nļothing in biology makes Phylogeny ,
Classification , Cladograms & sense except in the light of evolution " (
Dobzhansky ... Parsimony - one of several criteria that may be optimized in
building phylogenetic trees .

Author:

Publisher:

ISBN: UOM:39015064087078

Category: Biology

Page:

View: 206

Categories: Biology

Behavioral Ecology of Coral Reef Fishes at Spawning Aggregation Sites

Behavioral Ecology of Coral Reef Fishes at Spawning Aggregation Sites

I used the computer program PAUP * ( Swofford 1996 betatest version ) in
conjunction with the tree - building program MacClade ( Maddison & Maddison
1992 ) throughout my thesis work to build phylogenetic trees and test their
topologies .

Author: Gorka Sancho

Publisher:

ISBN: UCSD:31822009139148

Category: Coral reef fishes

Page: 254

View: 488

"This thesis is an extensive investigation of the behavioral and ecological relationships between spawning reef fishes, their predators, and various environmental parameters at spawning aggregation sites. Underwater observations of spawning activities by eleven reef fish species and the hunting behaviors of both piscivorous and planktivorous predators were made at Johnston Atoll (Central Pacific). The spawning of reef fishes was typically correlated with local changes in current direction and predatory risks in daytime-spawning species, showing responses designed to reduce the mortality of propagules and adults. Dusk-spawning species generally did not respond to changes in flow direction or predator abundance. Piscivores were most active at spawning sites during the daytime hours, when spawning prey fish were most abundant, but showed low activity at dusk, the period of highest prey diversity. Alternate hunting behaviors (midwater or ambush attacks) were used by piscivores when feeding on spawning fishes, and resulted in different capture success rates. The difference in heights of spawning ascents by two trunkfish species was interpreted to be the result of intraspecific competition among males, and could not be explained by interspecific differences in susceptibility to predation, estimated as a function' of the specific toxicity of both species. ."--Stinet.
Categories: Coral reef fishes

Science Culture

Science   Culture

another species , ii ) If one species is close to another STATISTICAL
APPROACHES IN BUILDING PHYLOGENETIC TREES WITH DNA AS
MOLECULAR MARKER * D. P. BURMA ** " The affinities of all the beings of the
same class have ...

Author:

Publisher:

ISBN: UOM:39015078450007

Category: Electronic journals

Page:

View: 356

Categories: Electronic journals