Guest Editor’s Introduction to the Special Section on Computational Biology and Bioinformatics (WABI 2005)—Part 2

IN this continuation of the special issue of papers invited from the Fifth International Workshop on Algorithms in Bioinformatics (WABI ’05), we present three papers which are summarized below. An alternative to the classical Hannenhali-Pevzner theory for sorting by reversal is described by Séverine Bérard, Anne Bergeron, Cedric Chauve, and Christophe Paul in their paper “Perfect Sorting by Reversal Is Not Always Difficult,” where the authors propose new algorithms for computing pairwise rearrangements that conserve the combinatorial structure of genomes. Ortholog detection is important in functional genome annotation. Akshay Vashist, Casimir A. Kulikowsky, and Ilya Muchnick present a new clustering algorithm on a weighted multipartite graph for automatically extracting groups of orthologous genes in their paper “Ortholog Clustering on a Multipartite Graph.” Cryo-Electron Microscopy (EM) is a powerful technique for low-resolution description of large macromolecule assemblies that are difficult to solve at the atomic level. The analysis of low resolution electron maps, however, may highlight components of complexes, as is shown in the paper “EMatch: Discovery of High Resolution Structural Homologues of Protein Domains in Intermediate Resolution Cryo-EM Maps” by Keren Lasker, Oranit Dror, Maxim Shatsky, Ruth Nussinov, and Haim J. Wolfson. The authors describe a novel integrated approach for recognizing structural homologues of protein domains present in a 610 A resolution cryo-EM map. Many thanks once again to the reviewers who helped make these issues possible.