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Comparative Genomics: Volume 1 2008 ed. [Mīkstie vāki]

  • Formāts: Paperback / softback, 546 pages, height x width: 229x152 mm, weight: 816 g, 3 Illustrations, color; 144 Illustrations, black and white; XIV, 546 p. 147 illus., 3 illus. in color., 1 Paperback / softback
  • Sērija : Methods in Molecular Biology 395
  • Izdošanas datums: 25-Dec-2011
  • Izdevniecība: Humana Press Inc.
  • ISBN-10: 1617377228
  • ISBN-13: 9781617377228
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  • Formāts: Paperback / softback, 546 pages, height x width: 229x152 mm, weight: 816 g, 3 Illustrations, color; 144 Illustrations, black and white; XIV, 546 p. 147 illus., 3 illus. in color., 1 Paperback / softback
  • Sērija : Methods in Molecular Biology 395
  • Izdošanas datums: 25-Dec-2011
  • Izdevniecība: Humana Press Inc.
  • ISBN-10: 1617377228
  • ISBN-13: 9781617377228
Citas grāmatas par šo tēmu:
Comparative Genomics, Volume 1, provides a collection of robust protocols for molecular biologists beginning to use comparative genomic analysis tools in a variety of areas. Volume I contains the first four of seven sections. In the first section, the reader is introduced to genomes via a number of visualization tools that allow one to browse through a particular genome of interest. The second and third sections deal with comparative analysis at the level of individual sequences, and present methods useful in sequence alignment, the discovery of conserved sequence motifs, and the analysis of codon usage. The fourth section deals with the identification and structural characterization of non-coding RNA genes this class of genes is particularly difficult to predict, and discovery of these elements is almost completely reliant on comparative genomics. Given the tremendous increase in available biosequence data over the past ten years, Comparative Genomics, Volume 1, is timely, comprehensive, and novel. A companion Volume 2 is also available from Humana Press.
Preface ix
Contributors xi
Part I Genome Visualization and Annotation
1 Comparative Analysis and Visualization of Genomic Sequences Using VISTA Browser and Associated Computational Tools
3(14)
Inna Dubchak
2 Comparative Genomic Analysis Using the UCSC Genome Browser
17(18)
Donna Karolchik
Gill Bejerano
Angie S. Hinrichs
Robert M. Kuhn
Webb Miller
Kate R. Rosenbloom
Ann S. Zweig
David Haussler
W. James Kent
3 Comparative Genome Analysis in the Integrated Microbial Genomes (IMG) System
35(22)
Victor M. Markowitz
Nikos C. Kyrpides
4 WebACT: An Online Genome Comparison Suite
57(18)
James C. Abbott
David M. Aanensen
Stephen D. Bentley
5 GenColors: Annotation and Comparative Genomics of Prokaryotes Made Easy
75(22)
Alessandro Romualdi
Marius Felder
Dominic Rose
Ulrike Gausmann
Markus Schilhabel
Gernot Glockner
Matthias Platzer
Jurgen Suhnel
6 Comparative Microbial Genome Visualization Using GenomeViz
97(12)
Rohit Ghai
Trinad Chakraborty
7 BugView: A Tool for Genome Visualization and Comparison
109(24)
David P. Leader
8 CGAS: A Comparative Genome Annotation System
133(16)
Kwangmin Choi
Youngik Yang
Sun Kim
Part II Sequence Alignments
9 BLAST QuickStart: Example-Driven Web-Based BLAST Tutorial
149(28)
David Wheeler
Medha Bhagwat
10 PSI-BLAST Tutorial
177(10)
Medha Bhagwat
L. Aravind
11 Organizing and Updating Whole Genome BLAST Searches with ReHAB
187(8)
David J. Esteban
Aijazuddin Syed
Chris Upton
12 Alignment of Genomic Sequences Using DIALIGN
195(10)
Burkhard Morgenstern
13 An Introduction to the Lagan Alignment Toolkit
205(16)
Michael Brudno
14 Aligning Multiple Whole Genomes with Mercator and MAVID
221(16)
Colin N. Dewey
15 Mulan: Multiple-Sequence Alignment to Predict Functional Elements in Genomic Sequences
237(18)
Gabriela G. Loots
Ivan Ovcharenko
16 Improving Pairwise Sequence Alignment between Distantly Related Proteins
255(16)
Jin-an Feng
Part III Identification of Conserved Sequences and Biases in Codon Usage
17 Discovering Sequence Motifs
271(24)
Timothy L. Bailey
18 Discovery of Conserved Motifs in Promoters of Orthologous Genes in Prokaryotes
295(14)
Rekin's lanky
Jacques van Helden
19 PhyME: A Software tool for Finding Motifs in Sets of Orthologous Sequences
309(10)
SaurabhSinha
20 Comparative Genomics-Based Orthologous Promoter Analysis Using the DoOP Database and the DoOPSearch Web Tool
319(10)
Endre Barta
21 Discovery of Motifs in Promoters of Coregulated Genes
329(20)
Olivier Sand
Jacques van Helden
22 Fastcompare: A Nonalignment Approach for Genome-Scale Discovery of DNA and mRNA Regulatory Elements Using Network-Level Conservation
349(18)
Olivier Elemento
Saeed Tavazoie
23 Phylogenetic Footprinting to Find Functional DNA Elements
367(14)
Austen R. D. Ganley
Takehiko Kobayashi
24 Detecting Regulatory Sites Using PhyloGibbs
381(22)
Rahul Siddharthan
Erik van Nimwegen
25 Using the Gibbs Motif Sampler for Phylogenetic Footprinting
403(22)
William Thompson
Sean Conlan
Lee Ann McCue
Charles E. Lawrence
26 Web-Based Identification of Evolutionary Conserved DNA cis-Regulatory Elements
425(12)
Panayiotis V. Benos
David L. Corcoran
Eleanor Feingold
27 Exploring Conservation of Transcription Factor Binding Sites with CON REAL
437(12)
Eugene Berezikov
Victor Guryev
Edwin Cuppen
28 Computational and Statistical Methodologies for ORFeome Primary Structure Analysis
449(16)
Gabriela Moura
Miguel Pinheiro
Adelaide Valente Freitas
Jose Luis Oliveira
Manuel A. S. Santos
Part IV Identification and Structural Characterization of Noncodinc RNAs
29 Comparative Analysis of RNA Genes: The caRNAc Software
465(10)
Helene Touzet
30 Efficient Annotation of Bacterial Genomes for Small, Noncoding RNAs Using the Integrative Computational Tool sRNAPredict2
475(14)
Jonathan Livny
31 Methods for Multiple Alignment and Consensus Structure Prediction of RNAs Implemented in MARNA
489(14)
Sven Siebert
Rolf Backofen
32 Prediction of Structural Noncoding RNAs With RNAz
503(24)
Stefan Washietl
33 RNA Consensus Structure Prediction With RNAalifold
527(18)
Ivo L. Hofacker
Index 545