Bioinformatics: A Practical Guide to the Analysis of Genes

"In this publication, Andy Baxevanis and Francis Ouellette . . . have undertaken the tough job of organizing the data during this box in a logical development and proposing it in a digestible shape. they usually have performed an outstanding task. This effective textual content will make a huge effect on organic examine and, in flip, on development in biomedicine. we're all of their debt."
-Eric Lander from the Foreword

Reviews from the 1st Edition

"...provides a extensive evaluate of the fundamental instruments for series research ... For biologists forthcoming this topic for the 1st time, it is going to be a truly important guide to maintain at the shelf after the 1st interpreting, as regards to the computer."
-Nature Structural Biology

"...should be within the own library of any biologist who makes use of the net for the research of DNA and protein series data."

"...a significant primer designed to navigate the amateur in the course of the intricacies of in scripto research ... The finished gene searcher also will locate this publication an invaluable addition to their library ... an outstanding connection with the foundations of bioinformatics."
-Trends in Biochemical Sciences

This re-creation of the hugely profitable Bioinformatics: a pragmatic advisor to the research of Genes and Proteins offers a valid origin of simple suggestions, with sensible discussions and comparisons of either computational instruments and databases suitable to organic learn.

Equipping biologists with the fashionable instruments essential to clear up sensible difficulties in series information research, the second one variation covers the large spectrum of subject matters in bioinformatics, starting from web techniques to predictive algorithms used on series, constitution, and expression info. With chapters written by way of specialists within the box, this updated reference completely covers very important suggestions and is acceptable for either the beginner and the skilled practitioner. Written in transparent, easy language, the ebook is on the market to clients with no a complicated mathematical or computing device technological know-how heritage. This new version contains:

  • All new end-of-chapter net assets, bibliographies, and challenge units
  • Accompanying site containing the solutions to the issues, in addition to hyperlinks to suitable internet assets
  • New assurance of comparative genomics, large-scale genome research, series meeting, and expressed series tags
  • A word list of widespread phrases in bioinformatics and genomics

Bioinformatics: a realistic advisor to the research of Genes and Proteins, moment variation is key studying for researchers, teachers, and scholars of all degrees in molecular biology and bioinformatics, in addition to for investigators excited by genomics, positional cloning, scientific learn, and computational biology.

Chapter 1 Bioinformatics and the web (pages 1–17): Andreas D. Baxevanis
Chapter 2 The NCBI info version (pages 19–43): James M. Ostell, Sarah J. Wheelan and Jonathan A. Kans
Chapter three The GenBank series (pages 45–63): Ilene Karsch?Mizrachi and B. F. Francis Ouellette
Chapter four filing DNA Sequences to the Databases (pages 65–81): Jonathan A. Kans and B. F. Francis Ouellette
Chapter five constitution Databases (pages 83–109): Christopher W. V. Hogue
Chapter 6 Genomic Mapping and Mapping Databases (pages 111–153): Peter S. White and Tara C. Matise
Chapter 7 details Retrieval from organic Databases (pages 155–185): Andreas D. Baxevanis
Chapter eight series Alignment and Database looking (pages 187–214): Gregory D. Schuler
Chapter nine construction and research of Protein a number of series Alignments (pages 215–232): Geoffrey J. Barton
Chapter 10 Predictive equipment utilizing DNA Sequences (pages 233–252): Andreas D. Baxevanis
Chapter eleven Predictive tools utilizing Protein Sequences (pages 253–282): Sharmila Banerjee?Basu and Andreas D. Baxevanis
Chapter 12 Expressed series Tags (ESTs) (pages 283–301): Tyra G. Wolfsberg and David Landsman
Chapter thirteen series meeting and completing tools (pages 303–322): Rodger Staden, David P. pass judgement on and James okay. Bonfield
Chapter 14 Phylogenetic research (pages 323–358): Fiona S. L. Brinkman and Detlef D. Leipe
Chapter 15 Comparative Genome research (pages 359–392): Michael Y. Galperin and Eugene V. Koonin
Chapter sixteen Large?Scale Genome research (pages 393–412): Paul S. Meltzer
Chapter 17 utilizing Perl to Facilitate organic research (pages 413–449): Lincoln D. Stein

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Extra info for Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Volume 43, Second Edition

Example text

Users can send E-mail messages in a format defining the action to be performed to remote computers known as servers; the servers will then perform the desired operation and E-mail back the results. Although this method is not interactive (in that the user cannot adjust parameters or have control over the execution of the method in real time), it does place the responsibility for hardware maintenance and software upgrades on the individuals maintaining the server, allowing users to concentrate on their results instead of on programming.

An anonymous FTP session is established with the molecular biology FTP server at the University of Indiana to download the CLUSTAL W alignment program. The user inputs are shown in boldface. 11 12 B I O I N F O R M AT I C S A N D T H E I N T E R N E T ‘‘gooey’’) to navigate through the UNIX directories on the FTP server. Users need not have any knowledge of UNIX commands to download files; instead, they select from pop-up menus and point and click their way through the UNIX file structure. The most popular FTP program on the Macintosh platform for FTP sessions is Fetch.

See text for details. 3. A screen dump of the gap4 Contig Selector, which gives an overview of the state of a sequencing project and provides a method for users to select contigs for processing. See text for details. 4. A screen dump of the gap4 Contig Comparator. This transformed version of the Contig Selector is used to display the results of analytical methods that give information about the relationships between contigs. For example, it can show sequence matches between contigs and the positions of read pairs that span contigs.

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