Introduction to Computational Genomics: A Case Studies Approach
Where did SARS come from? Have we inherited genes from Neanderthals? How do plants use their internal clock? The genomic revolution in biology enables us to answer such questions. But the revolution would have been impossible without the support of powerful computational and statistical methods that enable us to exploit genomic data. Many universities are introducing courses to train the next generation of bioinformaticians: biologists fluent in mathematics and computer science, and data analysts familiar with biology. This readable and entertaining book, based on successful taught courses, provides a roadmap to navigate entry to this field. It guides the reader through key achievements of bioinformatics, using a hands-on approach. Statistical sequence analysis, sequence alignment, hidden Markov models, gene and motif finding and more, are introduced in a rigorous yet accessible way. A companion website provides the reader with Matlab-related software tools for reproducing the steps demonstrated in the book.
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algorithm alignment score alphabet amino acid sequences amino acids analysis bioinformatics biological BLAST book’s website cell Chapter Chlamydia CLUSTALW clusters computational genomics contain databases dataset deﬁne Deﬁnition discussed DNA sequences efﬁcient eukaryotic evolution example eyeless ﬁeld ﬁnd ﬁrst frequency GC content GenBank gene family gene ﬁnding genetic code genetic distance genitalium genome sequence given global alignment Guangdong hidden Markov models HMMs homologous human hypothesis testing identiﬁed inﬂuenzae k-mers KA/KS length Markov chain matrix methods microarrays Molecular molecules motif mRNA mtDNA multinomial model multiple alignment mutations nodes non-synonymous nucleotide ORFs organisms orthologous pairwise alignment phylogenetic trees position preﬁx probability proﬁle prokaryotic proteins PSSM quence random sequences reading frame regions regulatory result SARS scoring function sequence alignment signiﬁcant similar simple species speciﬁc statistical stop codons substitution matrix substitutions synteny taxa threshold trace-back transcription virus viruses VIVALASVEGAS whole genome yeast