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 http:...