This introduction to computational molecular biology will help programmers and biologists learn the skills needed to start work in this important, expanding field. The author explains many of the basic computational problems and gives concise, working programs to solve them in the Perl programming language. With minimal prerequisites, the author explains the biological background for each problem, develops a model for the solution, then introduces the Perl concepts needed to implement the solution. The book covers pairwise and multiple sequence alignment, fast database searches for homologous sequences, protein motif identification, genome rearrangement, physical mapping, phylogeny reconstruction, satellite identification, sequence assembly, gene finding, and RNA secondary structure. The concrete examples and step-by-step approach make it easy to grasp the computational and statistical methods, including dynamic programming, branch-and-bound optimization, greedy methods, maximum likelihood methods, substitution matrices, BLAST searching, and Karlin-Altschul statistics. Perl code is provided on the accompanying CD.

Publisher description

The recent explosive growth of biological data has lead to a rapid increase in the number of molecular biology databases. Held in many different locations and often using varying interfaces and non-standard data formats, integrating and comparing data from these multiple databases can be difficult and time-consuming. This book provides an overview of the key tools currently available for large-scale comparisons of gene sequences and annotations, focusing on the databases and tools from the University of California, Santa Cruz (UCSC), Ensembl, and the National Centre for Biotechnology Information (NCBI). Written specifically for biology and bioinformatics students and researchers, it aims to give an appreciation of the methods by which the browsers and their databases are constructed, enabling readers to determine which tool is the most appropriate for their requirements. Each chapter contains a summary and exercises to aid understanding and promote effective use of these important tools.

This book provides a detailed and up-to-dated information on the genomes belonging to three major life forms on Earth – archaea, prokaryotes and eukaryotes. Each section describes about the genome of a specific group of organisms, such as viruses, archaea, bacteria, eukaryotes and organellar genomes. Individual chapters provide details of their organization, structure, evolution, sequencing strategies and functions. Further, this book discusses the technologies that are applied for genome sequencing; assembly, annotation and gene prediction. Other topics include the genomes of important model organisms, mitochondria genome of Neanderthal fossil, etc. This book also examines the evolution of chloroplast and mitochondria genomes by comparing with bacteria, addresses the diseases that occur in humans due to the mutations in mitochondrial genome, gene therapy and engineering of chloroplast and mitochondrial genomes. Lastly, it features an overview of the role of proteomics, exposomics, connectomics, metabolomics, and microbiomics. This book is a fascinating read for students, lecturers and researchers in the field of genetics, genomics, microbiology and life sciences.

Your research has generated gigabytes of data and now you need to analyse it. You hate using spreadsheets but it is all you know, so what else can you do? This book will transform how you work with large and complex data sets, teaching you powerful programming tools for slicing and dicing data to suit your needs. Written in a fun and accessible style, this step-by-step guide will inspire and inform non-programmers about the essential aspects of Unix and Perl. It shows how, with just a little programming knowledge, you can write programs that could save you hours, or even days. No prior experience is required and new concepts are introduced using numerous code examples that you can try out for yourself. Going beyond the basics, the authors touch upon many broader topics that will help those new to programming, including debugging and how to write in a good programming style.

Your author decided to write this book about Genome Mapping after attending a Dinner Lecture for Caltech Alumni living in the Santa Barbara County area of Mid-Coast California Dr David Barker, BS 1963 Caltech & PhD in Biochemistry from Brandeis University, gave a slide presentation on DNA sequencing and what it can tell you. In my quest for more knowledge about this exciting area of biochemistry, I sought more information about Genome Mapping and Entire DNA Sequencing from the Google and Yahoo search engines. As is common in Internet Research, I found a great deal of research was taking place worldwide. It was my objective to summarize this research in this book so my readers could learn what is happening and where to find more information about this important area of Biochemistry. One possibility is modifying your DNA to reduce susceptibility to certain diseases..perhaps we will be able to reduce our risk of cancer. One of my good friends died recently of Prostate Cancer, so my interest in combating Cancer has been intensified.

Genomics is a rapidly growing scientific field with applications ranging from improved disease resistance to increased rate of growth. Aquaculture Genome Technologies comprehensively covers the field of genomics and its applications to the aquaculture industry. This volume looks to bridge the gap between a basic understanding of genomic technology to its practical use in the aquaculture industry.