Comparative genomics. v. 2 / edited by Nicholas H. Bergman. — Totowa : Humana Press, c2007. – (58.17/M592/v.396)

Contents

    Table of Contents
    
    Preface ix
    Contributors xi
    PART 1: GENOME VISUALIZATION AND ANNOTATION
    1 Comparative Analysis and Visualization of Genomic Sequences Using VISTA Browser and Associated Computational Tools
    2 Comparative Genomic Analysis Using the UCSC Genome Browser
    3 Comparative Genome Analysis in the Integrated Microbial Genomes (IMG) System
    4 WebACT: An Online Genome Comparison Suite
    5 GenColors: Annotation and Comparative Genomics of Prokaryotes Made Easy
    6 Comparative Microbial Genome Visualization Using GenomeViz
    7 BugView: A Tool for Genome Visualization and Comparison
    8 CGAS: A Comparative Genome Annotation System
    PART 2: SEQUENCE ALIGNMENTS
    9 BLAST QuickStart: Example-Driven Web-Based BLAST Tutorial
    10 PSI-BLAST Tutorial
    11 Organizing and Updating Whole Genome BLAST Searches With ReHAB
    12 Alignment of Genomic Sequences Using DIALIGN
    13 An Introduction to the Lagan Alignment Toolkit
    14 Aligning Multiple Whole Genomes with Mercator and MAVID
    15 Mulan: Multiple-Sequence Alignment to Predict Functional Elements in Genomic Sequences
    16 Improving Pairwise Sequence Alignment between Distantly Related Proteins
    PART 3: IDENTIFiCATiON OF CONSERVED SEQUENCES AND BIASES IN CODON USAGE
    17 Discovering Sequence Motifs
    18 Discovery of Conserved Motifs in Promoters of Orthologous Genes in Prokaryotes
    19 PhyME: A Software tool for Finding Motifs in Sets of Orthologous Sequences
    20 Comparative Genomics-Based Orthologous Promoter Analysis Using the DoOP Database and the DoOPSearch Web Tool
    21 Discovery of Motifs in Promoters of Coregulated Genes
    22 Fastcompare: A Nonalignment Approach for Genome-Scale Discovery of DNA and mRNA Regulatory Elements Using Network-Level Conservation
    23 Phylogenetic Footprintingto Find Functional DNA Elements
    24 Detecting Regulatory Sites Using PhyloGibbs
    25 Using the Gibbs Motif Sampler for Phylogenetic Footprinting
    26 Web-Based Identification of Evolutionary Conserved DNA cis-Regulatory Elements
    27 Exploring Conservation of Transcription Factor Binding Sites with CONREAL
    28 Computational and Statistical Methodologies for ORFeome Primary Structure Analysis
    PART 4: IDENTIFICATION AND STRUCTURAL CHARACTERIZATION OF NONCODING RNAs
    29 Comparative Analysis of RNA Genes: The caRNAc Software
    30 Efficient Annotation of Bacterial Genomes for Small， Noncoding RNAs Using the Integrative Computational Tool sRNAPredict2
    31 Methods for Multiple Alignment and Consensus Structure Prediction of RNAs Implemented in MARNA
    32 Prediction of Structural Noncoding RNAs With RNAz
    33 RNA Consensus Structure Prediction With RNAalifold
    Index 545