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By L. R. Grate, C. Bhattacharyya, M. I. Jordan, I. S. Mian (auth.), Roderic Guigó, Dan Gusfield (eds.)

We are happy to provide the court cases of the second one Workshop on Al- rithms in Bioinformatics (WABI 2002), which happened on September 17-21, 2002 in Rome, Italy. The WABI workshop used to be a part of a three-conference me- ing, which, as well as WABI, integrated the ESA and APPROX 2002. the 3 meetings are together referred to as ALGO 2002, and have been hosted by means of the F- ulty of Engineering, collage of Rome “La Sapienza”. Seehttp://www.dis. uniroma1.it/˜algo02 for extra information. The Workshop on Algorithms in Bioinformatics covers study in all components of algorithmic paintings in bioinformatics and computational biology. The emphasis is on discrete algorithms that tackle vital difficulties in molecular biology, genomics,andgenetics,thatarefoundedonsoundmodels,thatarecomputati- best friend e?cient, and which were carried out and established in simulations and on actual datasets. The aim is to give contemporary study effects, together with signi?cant paintings in development, and to spot and discover instructions of destiny study. unique study papers (including signi?cant paintings in development) or sta- of-the-art surveys have been solicited on all facets of algorithms in bioinformatics, together with, yet now not restricted to: specified and approximate algorithms for genomics, genetics, series research, gene and sign reputation, alignment, molecular evolution, phylogenetics, constitution choice or prediction, gene expression and gene networks, proteomics, sensible genomics, and drug design.

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Extra resources for Algorithms in Bioinformatics: Second International Workshop, WABI 2002 Rome, Italy, September 17–21, 2002 Proceedings

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Given an input graph G as instance for either minEdgeBipartizer or minNodeBipartizer, we subdivide each edge into two edges in series. (The resulting graph G is clearly bipartite, we call SNPs the new nodes and fragments the old ones). Now, of the two edges incident with every SNP, we declare one to be odd and one to be even. Clearly, solving or approximating MSR on (G , ) amount to solving or approximating (within exactly the same approximation) minEdgeBipartizer on G. Moreover, solving or approximating MFR on (G , ) amounts to solving or approximating (within exactly the same approximation) minNodeBipartizer on G.

Simultaneous shotgun sequencing of multiple cDNA clones. DNA Seq. 7 (1997) 63–70 18. : Large-scale concatenation cDNA sequencing. Genome Res. 7 (1997) 353–358 19. : Analysing uncharted transcriptomes with SAGE. Trends Genet. 16 (2000) 423–425 Pooled Genomic Indexing (PGI) 27 Appendix Proof (Proposition 1). The number of random shotgun reads from the row pool associated with the clone equals cmL 2 . By Equation (1), the probability that at least one of them aligns with the reference sequence equals cmL cmL 2 M phit 2 M =1− 1− ≈ 1 − e−c 2 .

Large-scale concatenation cDNA sequencing. Genome Res. 7 (1997) 353–358 19. : Analysing uncharted transcriptomes with SAGE. Trends Genet. 16 (2000) 423–425 Pooled Genomic Indexing (PGI) 27 Appendix Proof (Proposition 1). The number of random shotgun reads from the row pool associated with the clone equals cmL 2 . By Equation (1), the probability that at least one of them aligns with the reference sequence equals cmL cmL 2 M phit 2 M =1− 1− ≈ 1 − e−c 2 . (4) m mL The probability that the row and column pools both generate reads aligning to the reference sequence equals p2≥1 , as claimed.

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