Bioinformatics provides in depth coverage of the principles and applications of bioinformatic analyses of nucleic acid and protein sequences, databases and data mining. Dynamic programming algorithms of Needleman-Wunsch and Smith-Waterman, amino acid exchange matrices such as Dayhoff PAM series matrices and BLOSSUM series matrices and DOT matrix are discussed in detail along with pair-wise sequence alignment tools such as BLAST, FASTA and their variants, multiple sequence alignment tools such as CLUSTAL-W, CLUSTAL-X, SAGA, and progressive alignment and profile alignment. The book describes methods of detection and prediction of genes, ORFs, promoters, motifs, mRNA, tRNA, miRNA, their structure and function and protein structure and function using ab initio HMM and Neural Networks. Software programs like GeneID, Genescan, Genie, GeneModeler, GRAIL and GeneMARK for gene detection and visual mining tools available are discussed while Gene Ontology (GO) and use of sequence information for phylogenetic inferences are illustrated.
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Data Mining 3 1
Analysis of Nucleotide Sequences 4 1
Analysis of Protein Sequences 5 1
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algorithm amino acid amino acid sequences amino acid substitution analysis annotation approach binding sites biological BLAST BLOSUM calculated cell cloning clusters coding regions coding sequence codon usage consensus sequence conserved contains defined deletions detect divergent DNA sequence elements encode eukaryotic evolution exons FASTA frequency function gap penalties gene prediction genetic genomic sequence homology identify identity input insertions interactions introns k-tuple length Markov model match matrix methods molecular motifs mRNA multiple alignment multiple sequence alignment mutations neural network nodes non-coding non-coding RNAs nucleic acid nucleotide nucleotide sequence occur optimal output pair-wise pairs parameters patterns phylogenetic position probability protein family protein sequence PSI-BLAST query sequence random reading frames refers regulatory related sequences relationships score secondary structure segments sequence comparison sequence data sequence database sequence similarity signals specific statistical stop codons tertiary structure transcription tree tRNA types weight window words