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Issue No. 06 - Nov.-Dec. (2013 vol. 10)
ISSN: 1545-5963
pp: 1403-1411
Yann Christinat , EPFL, Lab. for Comput. Biol. & Bioinf., Lausanne, Switzerland
Bernard M. E. Moret , EPFL, Lab. for Comput. Biol. & Bioinf., Lausanne, Switzerland
Alternative splicing is now recognized as a major mechanism for transcriptome and proteome diversity in higher eukaryotes, yet its evolution is poorly understood. Most studies focus on the evolution of exons and introns at the gene level, while only few consider the evolution of transcripts. In this paper, we present a framework for transcript phylogenies where ancestral transcripts evolve along the gene tree by gains, losses, and mutation. We demonstrate the usefulness of our method on a set of 805 genes and two different topics. First, we improve a method for transcriptome reconstruction from ESTs (ASPic), then we study the evolution of function in transcripts. The use of transcript phylogenies allows us to double the precision of ASPic, whereas results on the functional study reveal that conserved transcripts are more likely to share protein domains than functional sites. These studies validate our framework for the study of evolution in large collections of organisms from the perspective of transcripts; for this purpose, we developed and provide a new tool, TrEvoR.
Phylogeny, Human factors, Databases, Evolution (biology), Prediction algorithms

Y. Christinat and B. M. Moret, "A Transcript Perspective on Evolution," in IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 10, no. 6, pp. 1403-1411, 2014.
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