Sequence Data Analysis Guidebook / Edition 1

by Simon R. Swindell

Overview

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 chapters 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.

Product Details

ISBN-13:	9780896033580
Publisher:	Springer-Verlag New York, LLC
Publication date:	12/01/1996
Series:	Methods in Molecular Biology , #70
Edition description:	1997
Pages:	324
Product dimensions:	5.83(w) x 9.02(h) x 0.03(d)

About the Author

Swindell, Simon R. (Nottingham Univ)

The contributors represent the specialties of biological sciences, agricultural biotechnology, immmunology, and biochemistry. Most are from U.S. and U.K. research institutes, medical research and development companies, and universities, including Central Public Health Laboratory, EMBL Outstation-The EBI in Cambridge, and Rush Medical School.

Table of Contents

GeneJockeyll.- The Genetic Data Environment.- ABI Analysis.- SeqEd.- From ABI Sequence Data to LASERGENE’s EDITSEQ.- SEQMAN.- GeneJockeyll.- AutoAssembler Sequence Assembly Software.- MEGALIGN.- GeneJockeyII.- GeneJockeyII.- Sequence Navigator.- The European Bioinformatics Institute.- GeneAssist.- GENEMAN of LASERGENE.- GeneJockeyII.- GeneJockeyII.- GeneJockeyII.- PROTEAN.- MAPDRAW.- The Gene Construction Kit.- GeneJockeyII.- OLIGO.- PRIME.- PRIMERSELECT.- The European Bioinformatics Institute.

Editorial Reviews

Demonstrates how to examine the data produced by modern automated sequencers, how to assess its quality, how to remove extraneous data, and how to align multiple overlapping sequence fragments for either assembly into sequence contigs or comparison with similar sequences from different sources. Procedures for comparing newly derived sequences with the information in the sequence databases are covered, as are techniques for performing restriction analysis, calculating the translation products of open reading frames, and making detailed analyses of the expressed "proteins." Annotation c. by Book News, Inc., Portland, Or.

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