Get Foundations of comparative genomics PDF

By Arcady R. Mushegian

ISBN-10: 0120887940

ISBN-13: 9780120887941

This booklet offers an outline of computational research of genes and genomes, and of a few such a lot impressive findings that pop out of this paintings. Foundations of Comparative Genomics provides a old viewpoint, starting with early research of person gene sequences, to offer day comparability of gene repertoires encoded by means of thoroughly sequenced genomes. the writer discusses the underlying medical rules of comparative genomics, argues that of entirety of many genome sequences began a brand new period in biology, and gives a private view on a number of state of the art concerns, reminiscent of structures biology and whole-genome phylogenetic reconstructions. This publication is an important reference for researchers and scholars in computational biology, evolutionary biology, and genetics.
* provides an old review of genome biology and its achievements
* contains themes no longer lined in different books resembling minimum and ancestral genomes
* Discusses the evolutionary resilience of protein-coding genes and widespread practical convergence on the molecular level
* seriously reports horizontal gene move and different contentious issues
* Covers comparative virology as a a little bit ignored starting place of recent genome technology

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Additional resources for Foundations of comparative genomics

Example text

The term is in fact more than 150 years old, believed to be first proposed by Sir Richard Owen, the renowned British anatomist and paleontologist of the 19th century, to describe morphological traits derived from ancestral traits. Homology has separate meanings in other areas of science, such as cytogenetics, organic chemistry, and algebra, with which we will not concern ourselves here. Characters can be “genic” in the Pauling–Zuckerkandl sense (see Chapter 1)—that is, represent genes or sense-carrying units derived from genes.

Thus, A1C is to be understood as homologous copy 1 of gene A in species C. Timelines are indicated by T1–T4. Sp, speciation; Dp, duplication; Hgt, horizontal gene transfer; Gl, gene loss. Let us first sort orthologs from paralogs when the true evolutionary histories of species and genes are known (Fig. 1). A straightforward approach in this case is to detect all speciation points as well as all intralineage gene duplication points. A pair of genes produced by the speciation event are each others’ orthologs, and a pair of genes produced by the duplication event are each others’ paralogs.

First, after 20 years of gene sequencing and database searches, there were many more protein families than were available to the PAM project. Each of the families included more proteins, and there was much larger variation in the degree of protein identity within each family. More important, the BLOSUM project focused on selected fragments of multiple alignments, called blocks; these are not arbitrarily chosen fragments, nor are they leftovers of longer alignments. Blocks contain important information about proteins that PAM matrices were not able to reflect.

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Foundations of comparative genomics by Arcady R. Mushegian


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