Introduction to computational biology: an evolutionary approach
Analysis of molecular sequence data is the main subject of this introduction to computational biology. There are two closely connected aspects to biological sequences: (i) their relative position in the space of all other sequences, and (ii) their movement through this sequence space in evolutionary time. Accordingly, the first part of the book deals with classical methods of sequence analysis: pairwise alignment, exact string matching, multiple alignment, and hidden Markov models. In the second part evolutionary time takes center stage and phylogenetic reconstruction, the analysis of sequence variation, and the dynamics of genes in populations are explained in detail. In addition, the book contains a computer program with a graphical user interface that allows the reader to experiment with a number of key concepts developed by the authors.This textbook is intended for students enrolled in courses in computational biology or bioinformatics as well as for molecular biologists, mathematicians, and computer scientists.
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Optimal Pairwise Alignment
Biological Sequences and the Exact String Matching Problem
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Introduction to Computational Biology: An Evolutionary Approach
Bernhard Haubold,Thomas Wiehe
Eingeschränkte Leseprobe - 2006
a-globin alignment algorithms amino acids biology BLOSUM bootstrap calculated Chapter chromosome coalescent coding codon compared computed Consider contains corresponding distance distribution DNA sequence donor Drosophila dynamic programming dynamic programming matrix entries Equation estimate evolution evolutionary exact matches example exons expected number fixation FOXP2 function gene prediction genealogy genetic diversity genome given global alignment globin haplotypes Hence heterozygosity hidden Markov models homologous human input internal node intron labeled leghemoglobin linear loci locus melanogaster methods mismatches molecular clock multiple alignment multiple sequence alignment mutation rate neutral non-synonymous nucleotides number of segregating observed pair pairwise alignment parameters pattern phylogenetic phylogeny polymorphism population position probability protein sequences recent common ancestor recombination repeat residues root sample segregating sites selection sequence of length shown in Figure simulation SNPs species string matching substitution matrices substrings subtree suffix tree Table taxa topology traceback unrooted