Here are the refereed proceedings of the 6th International Workshop on Algorithms in Bioinformatics, WABI 2006, held in the course of the ALGO 2006 conference meetings. The book presents 36 revised full papers addressing all current issues of algorithms in bioinformatics, from mathematical tools to experimental studies of approximation algorithms and reports on significant computational analyses. For the first time, coverage extends to machine-learning approaches along with combinatorial optimization.

We are very pleased to present the proceedings of the First Workshop on Bio- formatics (WABI 2001), which took place in Aarhus on August 28{31, 2001, under the auspices of the European Association for Theoretical Computer S- ence (EATCS) and the Danish Center for Basic Research in Computer Science (BRICS). TheWorkshop onAlgorithmsinBioinformatics coversresearch onallaspects of algorithmic work in bioinformatics. The emphasis is on discrete algorithms that address important problems in molecular biology. These are founded on sound models, are computationally e cient, and have been implemented and tested in simulationsand on real datasets. The goal is to present recent research results, including signi cant work-in-progress, and to identify and explore dir- tions of future research. Speci c topics of interest include, but are not limited to: { Exactandapproximatealgorithmsforgenomics,sequence analysis,gene and signal recognition, alignment, molecular evolution, structure determination or prediction, gene expression and gene networks, proteomics, functional genomics, and drug design.{ Methods, software and dataset repositories for development and testing of such algorithms and their underlying models. { High-performance approaches to computationallyhardproblems inbioinf- matics, particularly optimization problems.

Here are the refereed proceedings of the 6th International Workshop on Algorithms in Bioinformatics, WABI 2006, held in the course of the ALGO 2006 conference meetings. The book presents 36 revised full papers addressing all current issues of algorithms in bioinformatics, from mathematical tools to experimental studies of approximation algorithms and reports on significant computational analyses. For the first time, coverage extends to machine-learning approaches along with combinatorial optimization.

We are very pleased to present the proceedings of the First Workshop on Bio- formatics (WABI 2001), which took place in Aarhus on August 28{31, 2001, under the auspices of the European Association for Theoretical Computer S- ence (EATCS) and the Danish Center for Basic Research in Computer Science (BRICS). TheWorkshop onAlgorithmsinBioinformatics coversresearch onallaspects of algorithmic work in bioinformatics. The emphasis is on discrete algorithms that address important problems in molecular biology. These are founded on sound models, are computationally e cient, and have been implemented and tested in simulationsand on real datasets. The goal is to present recent research results, including signi cant work-in-progress, and to identify and explore dir- tions of future research. Speci c topics of interest include, but are not limited to: { Exactandapproximatealgorithmsforgenomics,sequence analysis,gene and signal recognition, alignment, molecular evolution, structure determination or prediction, gene expression and gene networks, proteomics, functional genomics, and drug design.{ Methods, software and dataset repositories for development and testing of such algorithms and their underlying models. { High-performance approaches to computationallyhardproblems inbioinf- matics, particularly optimization problems.