Titlebook: Comparative Genomics; Volume 1 Nicholas H. Bergman Book 2008 Humana Press 2008 Bur.DNA.Evolution.Promoter.RNA.conservation.genes.primary st

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Comparative Genome Analysis in the Integrated Microbial Genomes (IMG) Systemalysis on a subset of genes, genomes, and functions of interest. IMG provides graphical viewers, summaries, and occurrence profile tools for comparing genes, pathways, and functions (terms) across specific genomes. Genes can be further examined using gene neighborhoods and compared with sequence alignment tools.

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PSI-BLAST Tutorial relationships between proteins. In this chapter, we discuss practical aspects of using PSI-BLAST and provide a tutorial on how to uncover distant relationships between proteins and use them to reach biologically meaningful conclusions.

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An Introduction to the Lagan Alignment Toolkits. This chapter provides an overview of the algorithms used by the LAGAN programs to construct genomic alignments, explains how to build alignments using either the standalone program or the web server, and discusses some of the common pitfalls users encounter when using the toolkit.

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Aligning Multiple Whole Genomes with Mercator and MAVIDfast and freely available, allowing researchers to perform genome alignments on a single laptop. This tutorial will guide the researcher through the steps required for whole-genome alignment with Mercator and MAVID.