Algorithms in bioinformatics

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The book contains a collection of papers focusing on various algorithms and methodologies in bioinformatics. Topics include reconstructing ancestral bacterial genomes, gene order reconstruction, and algorithms for sorting by reversals and transpositions. It presents polynomial-time algorithms for matching crossing contact-map patterns and approximations for sorting by transpositions and transreversals. The work also explores gapped local similarity searches, monotone scoring of patterns with mismatches, and suboptimal local alignments across multiple scoring schemes. Additionally, it discusses algorithms for estimating p-values, adding hidden nodes to gene networks, and joint analyses of DNA copy numbers and gene expression levels. The search for regulatory elements of alternative splicing events is addressed, alongside supervised learning for functional protein sequence annotation. The book also covers protein alignment, threading problems, protein-protein interfaces, and domain discovery in protein sequences. It includes discussions on haplotype inference, SNP haplotype reconstruction, and robust tag SNP selection. Other topics include RNA sequence alignment, translation initiation site prediction, phylogenetic tree consensus, and the relevance of 16S rDNA sequences. The collection concludes with methods for RNA secondary structure comparison and motif finding, emphasizing the integration of sample-driven and pattern-d