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this book present the proceedings of the 5th Workshop on Algorithmsin Bioinformatics (WABI 2005) which took place in Spain, 2005. The Workshop on Algorithms in Bioinformatics highlights research workspecifically developed to address algorithmic problems in biosequence analysis. The emphasis is therefore on statistical and probabilistic algorithms that addressimportant problems in the field of molecular and structural biology. the workshop aims to present recent research results, includingsignificant work in progress, and to identify and explore directions of futureresearch.Original research papers (including significant work in progress) or state-of-the-art surveys were solicited on all aspects of algorithms in bioinformatics,including, but not limited to: exact and approximate algorithms for genomics,genetics, sequence analysis, gene and signal recognition, alignment, molecularevolution, phylogenetics, structure determination or prediction, gene expressionand gene networks, proteomics, functional genomics, and drug design.