Download Sequence — Evolution — Function: Computational Approaches in by Eugene V. Koonin PDF

By Eugene V. Koonin

Sequence - Evolution - Function is an advent to the computational ways that play a serious position within the rising new department of biology often called practical genomics. The e-book offers the reader with an realizing of the foundations and methods of useful genomics and of the capability and boundaries of computational and experimental techniques to genome research.

Sequence - Evolution - Function may help bridge the "digital divide" among biologists and desktop scientists, permitting biologists to raised snatch the peculiarities of the rising box of Genome Biology and to benefit how you can enjoy the huge, immense quantity of series info to be had within the public databases. The e-book is non-technical with appreciate to the pc equipment for genome research and discusses those tools from the user's standpoint, with no addressing mathematical and algorithmic information. past functional familiarity with the elemental equipment for series research is an incredible virtue, yet a reader with out such adventure might be capable of use the publication as an creation to those tools. This ebook is ideal for introductory point classes in computational tools for comparative and practical genomics.

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Jejuni, Cj1591; C. trachomatis, CT786; E. coli, RpmJ; H. pylori, HP1297; L. lactis, Ll53863; M. leprae, MLl961; M. genitalium, MG174; R. , smlOO06; T. pallidum, TP0209; T. maritima, TM1476; V. cholerae, VC2575; X. fastidiosa, XF2440; Yeast, YPL183w. Bacterial and yeast proteins are from COG0257, other proteins are from GenPept and have the following gi numbers: rice O. sativa, gi12020; fmit fly D. melanogaster, CG18767; mouse, gi13559402; human, gi7677060. 28 Koonin and Galperin The functional convergence hypothesis would posit that sequence and structural similarities between proteins are observed because the shared features are strictly required for these proteins to perform their identical or similar functions.

Trachomatis, which have lost most of the pyrimidine biosynthesis genes, but still contain genes coding for the downstream steps ofthis pathway. 3. Lineage-specific expansion of gene families We have already mentioned the evolutionary importance of gene duplication leading to the emergence of paralogs, which may assume new functions, sometimes substantially different from those of the ancestral gene. Genome comparisons suggest that lineage-specific expansion of paralogous gene families, which in some cases account for a sizable fraction of a genome, is one of the major mechanisms of adaptation [408,506].

Strings of genes that are shared with at least one relatively distant genome [916]. As should be expected, this fraction gradually increases as new genomes are sequenced. A few operons that are conserved in distantly related prokaryotes consist of genes for ribosomal proteins and some other components of the translation machinery. Other conserved operons inc1ude those encoding subunits of the lf-ATPase and ABC-type transporter complexes [169,385,461,595]. 2. 4) shows that many pairs of closely related organisms have vastly different numbers of genes.

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