Bioinformatics: Sequence and Genome Analysis
The application of computational methods to DNA and protein science is a new and exciting development in biology. Bioinformatics: Sequence and Genome Analysis is a comprehensive introduction to this emerging field of study. The book has many unique and valuable features: It is written for any biologist who wants to understand methods of sequence and structure analysis and how the necessary computer programs work; Sequence alignment, structure prediction, phylogenetic and gene prediction, database searching, and genome analysis are clearly explained and amply illustrated; Underlying algorithms and assumptions are clearly explained for the non-specialist; Examples are presented in simple numerical terms rather than complex formulas and notation; Theoretical underpinnings are linked to biological problems and their solutions; Extensive tables provide descriptions and Web sources for a broad range of publicly available software; An associated Website (www.BioinformaticsOnline.org), accessible free of charge by book purchasers, provides links to Internet sources referred to in the text, as well as problem sets for classroom use, and other useful material not included in the text. Based on the author's extensive experience as a molecular geneticist and bioinformaticist at the University of Arizona, this is a uniquely educational book, ideal as a laboratory reference for investigators and also as teaching reference for graduate and undergraduate students studying this fast-changing discipline.
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Alignment of Pairs of Sequences
El Gene Prediction
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acid sequences aligned sequences alignment score Altschul amino acid amino acid substitution base pairs Biol BLAST blocks BLOSUM calculated changes CLUSTALW codon coli column database search database sequences Dayhoff distribution DNA sequences domains dot matrix dynamic programming example FASTA ﬁle ﬁnd ﬁnding ﬁrst frequency function gap penalties GenBank gene gene prediction genetic genomic sequences global alignment Henikoff hidden Markov models identiﬁed large number log odds scores matches method mismatches motif multiple sequence alignment mutation Nucleic Acids Nucleic Acids Res nucleotide number of sequences optimal alignment organisms patterns phylogenetic analysis possible probability produce proﬁle protein families protein sequence protein structures pseudocounts PSSM query sequence random sequences regions related sequences represent residues RNA secondary structure scoring matrix sequence analysis sequence positions sequence similarity server signiﬁcant similarity searches statistical structure prediction substitution matrices Table tree unrelated sequences variation