Algorithms in Bioinformatics

We are pleased to present the proceedings of the 5th Workshop on Algorithms in Bioinformatics (WABI 2005) which took place in Mallorca, Spain, October 3 6, 2005. The WABI 2005 workshop was part of the ?ve ALGO 2005 conf- ence meetings, which, in addition to WABI, included ESA, WAOA, IWPEC, and ATMOS. WABI 2005 was sponsored by EATCS (the European Assoc- tion for Theoretical Computer Science), the ISCB (the International Society for Computational Biology), the Universitat Polit` ecnica de Catalunya, the U- versitat de les Illes Balears, and the Ministerio de Educaci on y Ciencia. See wabi05/ for more details. The Workshop on Algorithms in Bioinformatics highlights research work speci?cally developed to address algorithmic problems in biosequence analysis. Theemphasisisthereforeonstatisticalandprobabilisticalgorithmsthataddress important problems in the ?eld of molecular and structural biology. At present, given the enormous scienti?c and technical e?orts in functional and structural genomics, the relevance of the problem is therefore constrained by the need for sound, e?cient and specialized algorithms, capable of achieving solutions that can be tested by the biological community. Indeed the ultimate goal is to - plement algorithms capable of extracting real features from real biological data sets. Therefore the workshop aims to present recent research results, including signi?cant work in progress, and to identify and explore directions of future research.

Inhalt
Expression.- Spectral Clustering Gene Ontology Terms to Group Genes by Function.- Dynamic De-Novo Prediction of microRNAs Associated with Cell Conditions: A Search Pruned by Expression.- Clustering Gene Expression Series with Prior Knowledge.- A Linear Time Biclustering Algorithm for Time Series Gene Expression Data.- Time-Window Analysis of Developmental Gene Expression Data with Multiple Genetic Backgrounds.- Phylogeny.- A Lookahead Branch-and-Bound Algorithm for the Maximum Quartet Consistency Problem.- Computing the Quartet Distance Between Trees of Arbitrary Degree.- Using Semi-definite Programming to Enhance Supertree Resolvability.- An Efficient Reduction from Constrained to Unconstrained Maximum Agreement Subtree.- Pattern Identification in Biogeography.- On the Complexity of Several Haplotyping Problems.- A Hidden Markov Technique for Haplotype Reconstruction.- Algorithms for Imperfect Phylogeny Haplotyping (IPPH) with a Single Homoplasy or Recombination Event.- Networks.- A Faster Algorithm for Detecting Network Motifs.- Reaction Motifs in Metabolic Networks.- Reconstructing Metabolic Networks Using Interval Analysis.- Genome Rearrangements.- A 1.375-Approximation Algorithm for Sorting by Transpositions.- A New Tight Upper Bound on the Transposition Distance.- Perfect Sorting by Reversals Is Not Always Difficult.- Minimum Recombination Histories by Branch and Bound.- Sequences.- A Unifying Framework for Seed Sensitivity and Its Application to Subset Seeds.- Generalized Planted (l,d)-Motif Problem with Negative Set.- Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI).- The Peres-Shields Order Estimator for Fixed and Variable Length Markov Models with Applications to DNA Sequence Similarity.- Multiple Structural RNA Alignmentwith Lagrangian Relaxation.- Faster Algorithms for Optimal Multiple Sequence Alignment Based on Pairwise Comparisons.- Ortholog Clustering on a Multipartite Graph.- Linear Time Algorithm for Parsing RNA Secondary Structure.- A Compressed Format for Collections of Phylogenetic Trees and Improved Consensus Performance.- Structure.- Optimal Protein Threading by Cost-Splitting.- Efficient Parameterized Algorithm for Biopolymer Structure-Sequence Alignment.- Rotamer-Pair Energy Calculations Using a Trie Data Structure.- Improved Maintenance of Molecular Surfaces Using Dynamic Graph Connectivity.- The Main Structural Regularities of the Sandwich Proteins.- Discovery of Protein Substructures in EM Maps.