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By Mohamed Ibrahim Abouelhoda, Enno Ohlebusch (auth.), Gary Benson, Roderic D. M. Page (eds.)

This e-book constitutes the refereed court cases of the 3rd foreign Workshop on Algorithms in Bioinformatics, WABI 2003, held in Budapest, Hungary, in September 2003.

The 36 revised complete papers awarded have been conscientiously reviewed and chosen from seventy eight submissions. The papers are geared up in topical sections on comparative genomics, database looking out, gene discovering and expression, genome mapping, development and motif discovery, phylogenetic research, polymorphism, protein constitution, series alignment, and string algorithms.

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Extra resources for Algorithms in Bioinformatics: Third International Workshop, WABI 2003, Budapest, Hungary, September 15-20, 2003. Proceedings

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Min(|p|, |q|)}. Proof. By definition an i-path can be extend in only one way which depends only on its last element. 22 G. Didier Theorem 2 An interval Ii (k) is i-complete if and only if it contains an i-path of order ri (sk ). Proof. By definition, if Ii (k) contains an i-path of order ri (sk ) = max{ri (sl )|l ∈ Ii (k)}, then it is complete. Reciprocally let us assume Ii (k) to be complete. We will proceed by induction over the length of an i-path of Ii (k). In particular, there is at least a position p1 ∈ Ii (k) such that ri (p1 ) and an i-path of order 1 belong to Ii (k).

Magnin, M. Giron, T. Dessingy, D. Ferrer, and J. Colinge. OLAV: General applicability of model-based MS/MS peptide score functions. In Proc. 51st Am. Soc. , Montreal, 2003. 16. A. L. McCormack et al. Direct analysis and identification of proteins in mixture by LC/MS/MS and database searching at the low-femtomole level. Anal. , 69:767–776, 1997. 17. R. E. Moore, M. K. Young, and T. D. Lee. Qscore: An algorithm for evaluating sequest database search results. J. Am. Soc. , 13:378–386, 2002. 18. I. A.

P. James. Mass Spectrometry. Proteome Research. Springer, Berlin, 2000. 11. R. S. Johnson et al. Collision-induced fragmentation of (m + h)+ ions of peptides. Side chain specific sequence ions. Intl. J. Mass Spectrom. and Ion Processes, 86:137–154, 1988. 12. A. Keller, A. I. Nesvizhskii, E. Kolker, and R. Aebersold. Empirical statistical model to estimate the accuracy of peptide identification made by MS/MS and database search. Anal. , 74:5383–5392, 2002. 13. A. Keller, S. Purvine, A. I. Nesvizhskii, S.

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