Sequence Data Analysis Guidebook

Fülszöveg

SEQUENCE DATA ANALYSIS GUIDEBOOK
Edited by
Simon R. Swindell
Nottingham University, Nottingham, UK
In Simon Swindell's eminently pratical Sequence Data Analysis Guidebook, leading researchers
concisely summarize their hands-on experiences and methods for successfully using the most popular
sequence analysis software packages on both desktop and mainframe machines. These experts demonstrate
how to examine the data produced by modern automated sequencers, how to assess their quality, how to
remove extraneous data, and how to align 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 massive amounts of information in the sequence databases are fully covered, as
are techniques for performing restriction analysis, searching for open reading frames, calculating the trans-
lation products of open reading frames, and making detailed... Tovább

Fülszöveg

SEQUENCE DATA ANALYSIS GUIDEBOOK
Edited by
Simon R. Swindell
Nottingham University, Nottingham, UK
In Simon Swindell's eminently pratical Sequence Data Analysis Guidebook, leading researchers
concisely summarize their hands-on experiences and methods for successfully using the most popular
sequence analysis software packages on both desktop and mainframe machines. These experts demonstrate
how to examine the data produced by modern automated sequencers, how to assess their quality, how to
remove extraneous data, and how to align 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 massive amounts of information in the sequence databases are fully covered, as
are techniques for performing restriction analysis, searching for open reading frames, calculating the trans-
lation products of open reading frames, and making detailed analyses of the expressed "proteins."
Sequence Data Analysis Guidebook promises to enable every researcher currently using molecular
biology to take control of all the essential computerized functions necessary to perform effective sequencing
today, whether it be sequence analysis, primer design, the production of complex publication-quality figures,
or the submission of published sequences to a major data bank.
FEATURES
Includes complete hands-on tutorials for the
leading sequence analysis software packages
Facilitates use of the ABI DNA Sequencer,
Genejockeyll, GENEMAN, MAPDRAW, OLIGO,
and other popular computer programs
Shows how to create detailed graphic
representations of restriction sites, coding
regions, and promoters
Helps create simulations of electrophoretic
patterns from digested DNA or protein
Aids in primer design either for continued
sequencing or for PCR manipulation of
analyzed sequences
Demonstrates how to successfully produce
complex, publication-quality figures
Explains how to submit published sequences to
the major data banks
Offers many protocols by their original
developers, with input from experienced users
CONTENTS
Genejockeyll: Entering and Editing Sequences. The Genetic
Data Environment: A User Modifiable and Expandable Mul-
tiple Sequence Analysis Package. ABI Analysis: Manipulation
of Sequence Data from the ABI DNA Sequencer. SeqEd:
Manipulation of Sequence Data and Chromatograms from the
ABI DNA Sequencer Analysis Files. From ABI Sequence Data
to LASERGENE'S EDITSEQ. SEQMAN: Contig Assembly. Gene-
jockeyll: DNA Sequencing and Fragment Assembly. Auto-
Assembler Sequence Assembly Software. MEGALIGN: The Mul-
tiple Alignment Module ofLASERGENE. Genejockeyll: Pairwise
Sequence Comparison. Genejockeyll: Multiple Alignment of
Homologous Sequences. Sequence Navigator: Multiple Sequence
Alignment Software. The European Bioinformatics Institute:
Network Services. Gene Assist: Smith-Waterman and Other Da-
tabase Similarity Searches and Identification of Motifs.
GENEMAN of LASERGENE. Genejockeyll: Database Search-
ing. Genejockeyll: Restriction Analysis. Genejockeyll:
Translation and Open Reading Frame Analysis. PROTEAN: Pro-
tein Sequence Analysis and Prediction. MAPDRAW: Restriction
Mapping and Analysis. The Gene Construction Kit: DNA
Sequence Analysis and Presentation. Genejockeyll: Primer
Design. OLIGO: Primer Selection. PRIME: Primer Selection.
PRIMERSELECT: Primer and Probe Design. The European Bio-
informatics Institute: Submission and Updating of Sequence
Databases. Index.
ISBN 0-89603-358-9
Methods in Molecular BiologyrM • 70
SEQUENCE DATA ANALYSIS GUIDEBOOK
ISBN: 0-89603-358-9
978089603358090000 Vissza