Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins
Format: PDF / Kindle (mobi) / ePub
Reviews of the Second Edition
"In this book, Andy Baxevanis and Francis Ouellette . . . have undertaken the difficult task of organizing the knowledge in this field in a logical progression and presenting it in a digestible form. And they have done an excellent job. This fine text will make a major impact on biological research and, in turn, on progress in biomedicine. We are all in their debt."
--Eric Lander, from the Foreword to the Second Edition
"The editors and the chapter authors of this book are to be applauded for providing biologists with lucid and comprehensive descriptions of essential topics in bioinformatics. This book is easy to read, highly informative, and certainly timely. It is most highly recommended for students and for established investigators alike, for anyone who needs to know how to access and use the information derived in and from genomic sequencing projects."
--Trends in Genetics
"It is an excellent general bioinformatics text and reference, perhaps even the best currently available . . . Congratulations to the authors, editors, and publisher for producing a weighty, authoritative, readable, and attractive book."
--Briefings in Bioinformatics
"This book, written by the top scientists in the field of bioinformatics, is the perfect choice for every molecular biology laboratory."
--The Quarterly Review of Biology
This fully revised version of a world-renowned bestseller provides readers with a practical guide covering the full scope of key concepts in bioinformatics, from databases to predictive and comparative algorithms. Using relevant biological examples, the book provides background on and strategies for using many of the most powerful and commonly used computational approaches for biological discovery. This Third Edition reinforces key concepts that have stood the test of time while making the reader aware of new and important developments in this fast-moving field. With a new full-color and enlarged page design, Bioinformatics, Third Edition offers the most readable, up-to-date, and thorough introduction to the field for biologists.
This new edition features:
* New chapters on genomic databases, predictive methods using RNA sequences, sequence polymorphisms, protein structure prediction, intermolecular interactions, and proteomic approaches for protein identification
* Detailed worked examples illustrating the strategic use of the concepts presented in each chapter, along with a collection of expanded,more rigorous problem sets suitable for classroom use
* Special topic boxes and appendices highlighting experimental strategies and advanced concepts
* Annotated reference lists, comprehensive lists of relevant Web resources, and an extensive glossary of commonly used terms in bioinformatics, genomics, and proteomics
Bioinformatics, Third Edition is essential reading for researchers, instructors, and students of all levels in molecular biology and bioinformatics, as well as for investigators involved in genomics, clinical research, proteomics, and computational biology.
...................... Appendix 3.3 Example of a Record in CON Division ............... 49 58 58 59 59 59 61 63 SUBMITTING DNA SEQUENCES TO THE DATABASES 65 Jonathan A. Kans and B. F. Francis Ouellette 5 Introduction .............................................................................. Why, Where, and What to Submit? ............................................. DNA/RNA ................................................................................ Population, Phylogenetic, and
feature points to the protein product Bioseq, which Entrez can also retrieve. The links in the data model allow retrieval of linked records at the touch of a button. The Genomes division in Entrez takes further advantage of the data model by providing ‘‘on the ﬂy’’ display of certain regions of large genomes, as is the case when one hits the ProtTable button in Web Entrez. Sequin Sequin is a submission tool that takes raw sequence data and other biological information and assembles a record
much attention is devoted to making sure they are valid. (If a translation is present in a GenBank record, there are valid coordinates present that can direct the translation of nucleotide sequence.) These sequences are the starting material for the protein databases and offer the most sensitive way of making new gene discoveries (Chapter 8). Because these annotations can be validated, they have added value, and having the correct identiﬁers also becomes important. The correct product name, or
of a protein in a PDB record using only the implicit sequence, ignoring the explicit SEQRES information. If this software then is asked to print the sequence of certain incomplete molecules, it will produce a nonphysiological and biologically irrelevant sequence. The implicit sequence, therefore, is not sufﬁcient to reconstruct the complete chemical graph. Consider an example in which the sequence ELVISISALIVES is represented in the SEQRES entry of a hypothetical PDB ﬁle, but the coordinate
includes information on mouse genetic markers and nomenclature, molecular segments (probes, primers, YACs and MIT primers), phenotypes, comparative mapping data, graphical displays of linkage, cytogenetic, and physical maps; experimental mapping data, and strain distribution patterns for recombinant inbred strains (RIs) and cross haplotypes. As of November 2000, there were over 29,500 genetic markers and 11,600 genes in MGD, with 85% and 70% of these placed onto the mouse genetic map,