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A Method of Consolidating and Combining EST and mRNA Alignments to a Genome to Enumerate Supported Splice Variants

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Algorithms in Bioinformatics (WABI 2002)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2452))

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Abstract

Many researchers have focused their attention on alternative splice forms of genes as a means to explain the apparent complexity of human and other higher eukaryotic organisms. The exon-intron structure implied by aligning ESTs and mRNAs to genomic sequence provides a useful basis for comparing different splice forms. There are software tools that enumerate all possible exon-intron combinations implied by these alignments, but this approach has potential drawbacks including a combinatorial explosion in the number of splice forms and the generation of many unsupported splice forms. altMerge retains information about exon combinations present in the input alignments. It uses this information to combine compatible subsets of the alignments into a single representative form. Substructures of these representative forms are then exchanged to enumerate only those alternative splice forms that are consistent with the input alignments.

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References

  1. Helt, G., Harvey, D. (Affymetrix): Personal communication. (2000)

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  2. Kan, Z., Rouchka, E., Gish, W., States, D.: Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. Genome Res. 11 (2001) 889–900.

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  3. Kent, J. (University of California at Santa Cruz): altGraph. Personal communication. (2000).

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  4. Mironov, A., Fickett, J., Gelfand, M.: Frequent alternative splicing of human genes. Genome Research 9 (1999) 1288–1293.

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  5. Schmucker et al.: Drosophila dscam is an axon guidance receptor exhibiting extraordinary molecular diversity. Cell 101 (2000) 671–684.

    Article  Google Scholar 

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© 2002 Springer-Verlag Berlin Heidelberg

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Wheeler, R. (2002). A Method of Consolidating and Combining EST and mRNA Alignments to a Genome to Enumerate Supported Splice Variants. In: Guigó, R., Gusfield, D. (eds) Algorithms in Bioinformatics. WABI 2002. Lecture Notes in Computer Science, vol 2452. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45784-4_15

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  • DOI: https://doi.org/10.1007/3-540-45784-4_15

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-44211-0

  • Online ISBN: 978-3-540-45784-8

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