Minimum Factorization Agreement of Spliced ESTs -- Annotating Fragmentation Patterns -- biRNA: Fast RNA-RNA Binding Sites Prediction -- Quantifying Systemic Evolutionary Changes by Color Coding Confidence-Scored PPI Networks -- PMFastR: A New Approach to Multiple RNA Structure Alignment -- On the Upper Bound of the Prediction Accuracy of Residue Contacts in Proteins with Correlated Mutations: The Case Study of the Similarity Matrices -- Constructing Majority-Rule Supertrees -- SCJ: A Variant of Breakpoint Distance for Which Sorting, Genome Median and Genome Halving Problems Are Easy -- A Simple, Practical and Complete -Time Algorithm for RNA Folding Using the Four-Russians Speedup -- Back-Translation for Discovering Distant Protein Homologies -- A Markov Classification Model for Metabolic Pathways -- Mimosa: Mixture Model of Co-expression to Detect Modulators of Regulatory Interaction -- Phylogenetic Comparative Assembly -- K-Partite RNA Secondary Structures -- Efficient Algorithms for Analyzing Segmental Duplications, Deletions, and Inversions in Genomes -- Predicting Gene Structures from Multiple RT-PCR Tests -- A Tree Based Method for the Rapid Screening of Chemical Fingerprints -- Generalizing the Four Gamete Condition and Splits Equivalence Theorem: Perfect Phylogeny on Three State Characters -- Decoding Synteny Blocks and Large-Scale Duplications in Mammalian and Plant Genomes -- A General Framework for Local Pairwise Alignment Statistics with Gaps -- mpscan: Fast Localisation of Multiple Reads in Genomes -- Fast Prediction of RNA-RNA Interaction -- FlexSnap: Flexible Non-sequential Protein Structure Alignment -- A Non-parametric Bayesian Approach for Predicting RNA Secondary Structures -- Exact Score Distribution Computation for Similarity Searches in Ontologies -- Linear-Time Protein 3-D Structure Searching with Insertions and Deletions -- Visualizing Phylogenetic Treespace Using Cartographic Projections -- A Simulation Study Comparing Supertree and Combined Analysis Methods Using SMIDGen -- Aligning Biomolecular Networks Using Modular Graph Kernels -- MADMX: A Novel Strategy for Maximal Dense Motif Extraction -- Large-Scale Neighbor-Joining with NINJA -- A Unifying View on Approximation and FPT of Agreement Forests -- Structural Alignment of RNA with Complex Pseudoknot Structure -- Improving Inference of Transcriptional Regulatory Networks Based on Network Evolutionary Models.

This book constitutes the refereed proceedings of the 9th International Workshop on Algorithms in Bioinformatics, WABI 2009, held in Philadelphia, USA, in September 2009. The 34 revised full papers presented together with the abstract of a keynote talk were carefully reviewed and selected from 90 submissions. All current issues of algorithms in bioinformatics are addressed, reaching from mathematical tools to experimental studies of approximation algorithms and reports on significant computational analyses. The topics range in biological applicability from gene interaction networks, molecular phylogeny, RNA and protein structure, and genome evolution.