Comparative Genomics
Volume 1
(Sprache: Englisch)
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...
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Klappentext zu „Comparative Genomics “
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.
Inhaltsverzeichnis zu „Comparative Genomics “
Comparative Genomics-Volume ITable of ContentsSection I-Genome Visualization and Annotation1. Comparative analysis and visualization of genomic sequences usingVISTA Browser and associated computational toolsInna Dubchak2. Comparative Genomic Analysis Using the UCSC Genome BrowserDonna Karolchik, Gill Bejerano, Angie S. Hinrichs, Robert M. Kuhn, WebbMiller, Kate R. Rosenbloom, Ann S. Zweig, David Haussler, W. James Kent3. Comparative Genome Analysis in the Integrated Microbial Genomes(IMG) SystemVictor M. Markowitz and Nikos C. Kyrpides4. WebACT: An Online Genome Comparison SuiteJames C. Abbott, David M. Aanensen, and Stephen D. Bentley5. GenColors: Annotation and Comparative Genomics of Prokaryotes madeeasyAlessandro Romualdi, Marius Felder, Dominic Rose, Ulrike Gausmann,Markus Schilhabel, Gernot Glöckner, Matthias Platzer, and Jürgen Sühnel6. Comparative Microbial Genome Visualization Using GenomeVizRohit Ghai and Trinad Chakraborty7. BugView: A Tool for Genome Visualization and ComparisonDavid P. Leader8. CGAS: Comparative Genome Annotation SystemKwangmin Choi, Youngik Yang, and Sun KimSection II-Sequence Alignments9. BLAST Quick Start: An Example-driven Web-based BLAST TutorialDavid Wheeler and Medha Bhagwat10. Psi-BLAST TutorialMedha Bhagwat, L. Aravind11. Organizing and Updating Whole Genome BLAST Searches with REHABDavid J. Esteban, Aijazuddin Syed, Chris Upton12. Alignment of Genomic Sequences Using DIALIGNBurkhard Morgenstern13. An Introduction to the Lagan Alignment ToolkitMichael Brudno14. Aligning Multiple Whole Genomes with Mercator and MavidColin N. Dewey15. Mulan: Multiple-Sequence Alignment to Predict Functional Elementsin Genomic SequencesGabriela G. Loots and Ivan Ovcharenko16. Improving Pairwise Sequence Alignment between Distantly RelatedProteinsJin-anFengSection III-Identification of Conserved Sequences and Biases in CodonUsage17. Discovering Sequence MotifsTimothy L. Bailey18. Discovery of conserved motifs in promoters of orthologous genes
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inprokaryotesRekin's Janky and Jacques van Helden19. PhyME: A Software Tool for Finding Motifs in Sets of OrthologousSequencesSaurabh Sinha20. Comparative Genomics-based Orthologous Promoter Analysis using theDoOP database and the DoOPSearch web toolEndre Barta21. Discovery of motifs in promoters of co-regulated genesOlivier Sand and Jacques van Helden22. Fastcompare: A non-alignment approach for genome-scale discoveryof DNA and mRNA regulatory elements using network-level conservationOlivier Elemento and Saeed Tavazoie23. Phylogenetic footprinting to find functional DNA elementsAusten R. D. Ganley and Takehiko Kobayashi24. Detecting Regulatory Sites using PhyloGibbsRahul Siddharthan and Erik Van Nimwegen25. Using the Gibbs Motif Sampler for Phylogenetic FootprintingWilliam Thompson, Sean Conlan, LeeAnn McCue, Charles E. Lawrence26. Web-based Identification of Evolutionary Conserved DNAcis-regulatory elementsPanayiotis V. Benos, David L. Corcoran, Eleanor Feingold27. Exploring conservation of transcription factor binding sites withCONREALEugene Berezikov, Victor Guryev, Edwin Cuppen28. Computational and Statistical Methodologies for Orfeome PrimaryStructure AnalysisGabriela Moura, Miguel Pinheiro, Adelaide Valente Freitas, Jose LuisOliveira, and Manuel A. S. SantosSection IV-Identification and Structural Characterization of non-codingRNAs29. Comparative analysis of RNA genes: the caRNAc softwareHélène Touzet30. Efficient annotation of bacterial genomes for small, non-codingRNAs using the integrative computational tool sRNAPredict2Jonathan Livny31. Methods for Multiple Alignment and
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Bibliographische Angaben
- 2007, 2008, 546 Seiten, mit farbigen Abbildungen, Maße: 16 x 24,1 cm, Gebunden, Englisch
- Herausgegeben:Bergman, Nicholas H.
- Herausgegeben: Nicholas H. Bergman
- Verlag: Humana Press
- ISBN-10: 1588296938
- ISBN-13: 9781588296931
- Erscheinungsdatum: 29.11.2007
Sprache:
Englisch
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