Tag: Bioinformatics

April 26, 2024

XML for Bioinformatics

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Free Download XML for Bioinformatics by Ethan Cerami
English | PDF (True) | 2005 | 311 Pages | ISBN : 0387230289 | 5.5 MB
Introduction The goal of this book is to introduce XML to a bioinformatics audience. It does so by introducing the fundamentals of XML, Document Type De?nitions (DTDs), XML Namespaces, XML Schema, and XML parsing, and illustrating these concepts with speci?c bioinformatics case studies. The book does not assume any previous knowledge of XML and is geared toward those who want a solid introduction to fundamental XML concepts. The book is divided into nine chapters: Chapter 1: Introduction to XML for Bioinformatics. This chapter provides an introduction to XML and describes the use of XML in biological data exchange. A bird’s-eye view of our ?rst case study, the Distributed Annotation System (DAS), is provided and we examine a sample DAS XML document. The chapter concludes with a discussion of the pros and cons of using XML in bioinformatic applications. Chapter 2: Fundamentals of XML and BSML. This chapter introduces the fundamental concepts of XML and the Bioinformatic Sequence Markup Language (BSML). We explore the origins of XML, de?ne basic rules for XML document structure, and introduce XML Na- spaces. We also explore several sample BSML documents and visualize these documents in the TM Rescentris Genomic Workspace Viewer.

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February 2, 2024

Genomic Perl From Bioinformatics Basics to Working Code

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Free Download Genomic Perl: From Bioinformatics Basics to Working Code By Rex A. Dwyer
2002 | 352 Pages | ISBN: 052180177X | PDF | 15 MB
In this introduction to computational molecular biology, Rex Dwyer explains many basic computational problems and gives concise, working programs to solve them in the Perl programming language. With minimal prerequisites, he covers the biological background for each problem, develops a model for the solution, and then introduces the Perl concepts needed to implement the solution. The chapters discuss 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. Concrete examples and a step-by-step approach enable readers to grasp the computational and statistical methods.

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