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Inferring transcript phylogenies.
Journal article

Inferring transcript phylogenies.

  • Christinat Y Laboratory of Computational Biology and Bioinformatics, EPFL, 1015 Lausanne, Switzerland. yann.christinat@epfl.ch
  • Moret BM
  • 2012-07-27
Published in:
  • BMC bioinformatics. - 2012
Algorithms
Alternative Splicing
Animals
Evolution, Molecular
Exons
Eye Proteins
Homeodomain Proteins
Humans
Introns
Models, Genetic
Myelin-Associated Glycoprotein
PAX6 Transcription Factor
Paired Box Transcription Factors
Phylogeny
Repressor Proteins
English Alternative splicing, an unknown mechanism 20 years ago, is now recognized as a major mechanism for proteome and transcriptome diversity, particularly in mammals–some researchers conjecture that up to 90% of human genes are alternatively spliced. Despite much research on exon and intron evolution, little is known about the evolution of transcripts. In this paper, we present a model of transcript evolution and an associated algorithm to reconstruct transcript phylogenies. The evolution of the gene structure–exons and introns–is used as basis for the reconstruction of transcript phylogenies. We apply our model and reconstruction algorithm on two well-studied genes, MAG and PAX6, obtaining results consistent with current knowledge and thereby providing evidence that a phylogenetic analysis of transcripts is feasible and likely to be informative.
Language
  • English
Open access status
gold
Identifiers
Persistent URL
https://sonar.ch/global/documents/22091
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