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作者 Schreiber, David R
書名 The bioinformaticist's toolbox in the post-genomic age: Applications and developments
國際標準書號 9780549101703
book jacket
說明 151 p
附註 Source: Dissertation Abstracts International, Volume: 68-06, Section: B, page: 3772
Adviser: Steven A. Benner
Thesis (Ph.D.)--University of Florida, 2007
Bioinformaticists of the post-genomic age, having at their disposal the complete sequence of the human genome, find themselves in possession of a true embarrassment of riches---a massive collection of data that grows ever larger with each new submission. To effectively mine this glut of information, the tools of bioinformatics must adapt, and new ones must be developed, tested and applied. Herein we describe a modification of a method, first developed by Pamilo, Bianchi, and Li for estimating mutation rates between the protein sequences from two extant species which allows for comparisons with proteins from ancestral species. In this case, the ancestral sequences are determined by parsimony, but the method is applicable to any phylogenetic method used to deduce ancestral states from extant species data. Computationally cheap, the parsimony method lends itself to the analysis of large datasets. We conducted such an experiment on a version of the GenBank database. The results were collected in a new database called The Adaptive Evolutionary Database (TAED), whose purpose was to be a collection of proteins that have rapidly (and presumably adaptively) evolved at some point in their natural history. In addition to discovering adaptive episodes, we used this method to search for compensatory covariation signals within another large database of sequences---signals that provide clues relating to the proteins' higher-order structures. These methods are used as well in interdisciplinary investigations that incorporate information from the paleontological and geological records. This provided high-level functional information relating to cytochrome P450 aromatases and their role in Suoidea evolution
School code: 0070
DDC
Host Item Dissertation Abstracts International 68-06B
主題 Biology, Genetics
Chemistry, Biochemistry
Biology, Bioinformatics
0369
0487
0715
Alt Author University of Florida
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