Sequence Data Analysis Guidebook

  • Simon R. Swindell

Part of the Methods In Molecular Medicine™ book series (MIMB, volume 70)

Table of contents

  1. Front Matter
    Pages i-ix
  2. Phil Taylor
    Pages 1-11
  3. Jonathan A. Eisen
    Pages 13-38
  4. Tracy L. Hagemann, Sau-Ping Kwan
    Pages 39-54
  5. Tracy L. Hagemann, Sau-Ping Kwan
    Pages 55-63
  6. Catherine Arnold, Jonathan P. Clewley
    Pages 65-74
  7. Simon R. Swindell, Thomas N. Plasterer
    Pages 75-89
  8. Phil Taylor
    Pages 91-106
  9. Steven R. Parker
    Pages 107-117
  10. Jonathan P. Clewley, Catherine Arnold
    Pages 119-129
  11. Phil Taylor
    Pages 131-136
  12. Phil Taylor
    Pages 137-143
  13. Steven R. Parker
    Pages 145-154
  14. Tomas P. Flores, Robert A. Harper
    Pages 155-171
  15. Eugene G. Shpaer
    Pages 173-187
  16. Jonathan P. Clewley
    Pages 189-196
  17. Phil Taylor
    Pages 197-212
  18. Phil Taylor
    Pages 213-219
  19. Phil Taylor
    Pages 221-225
  20. Thomas N. Plasterer
    Pages 227-239
  21. Thomas N. Plasterer
    Pages 241-256
  22. Bruce R. Troen
    Pages 257-272
  23. Phil Taylor
    Pages 273-278
  24. Juan Jose Estruch
    Pages 279-285
  25. Juan Jose Estruch
    Pages 287-290
  26. Thomas N. Plasterer
    Pages 291-302
  27. Tomas P. Flores, Benny Shomer
    Pages 303-317
  28. Back Matter
    Pages 319-324

About this book


Computers have revolutionized the analysis of sequencing data. It is unlikely that any sequencing projects have been performed in the last few years without the aid of computers. Recently their role has taken a further major step forward. Computers have become smaller and more powerful and the software has become simpler to use as it has grown in sophistication. This book reflects that change since the majority of packages described here are designed to be used on desktop computers. Computer software is now available that can run gels, collect data, and assess its accuracy. It can assemble, align, or compare multiple fragments, perform restriction analyses, identify coding regions and specific motifs, and even design the primers needed to extend the sequencing. Much of this soft­ ware may now be used on relatively inexpensive computers. It is now possible to progress from isolate d DNA to database submission without writing a single base down. To reflect this progression, the chapters in our Sequence Data Analysis Guidebook are arranged, not by software package, but by fimction. The early chapters deal with examining the data produced by modem automated sequenc­ ers, assessing its quality, and removing extraneous data. The following chap­ ters describe the process of aligning multiple sequences in order to assemble overlapping fragments into sequence contigs to compare similar sequences from different sources. Subsequent chapters describe procedures for compar­ ing the newly derived sequence to the massive amounts of information in the sequence databases.

Editors and affiliations

  • Simon R. Swindell
    • 1
  1. 1.Department of Biochemistry, Queen’s Medical CeneterNottingham UniversityNottinghamUK

Bibliographic information

  • DOI
  • Copyright Information Humana Press 1997
  • Publisher Name Springer, Totowa, NJ
  • eBook Packages Springer Protocols
  • Print ISBN 978-0-89603-358-0
  • Online ISBN 978-1-59259-556-3
  • Series Print ISSN 1064-3745
  • Series Online ISSN 1940-6029
  • Buy this book on publisher's site
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