GSoC 2010: Implementing SDI Project Updates:


Some useful references for our “Implementation of algorithm to infer gene duplications in BioRuby” proposal.

SDI algorithm:

Classic paper on the significance of gene duplications, phylogenomics:

Orthologs, paralogs, xenologs:

Definition of gene duplication and the mapping function “M”:

  • Goodman,M.,  Czelusniak,J.,  Moore,G.W.,  Romero-Herrera,A.E.
    and Matsuda,G. (1979) Fitting the gene lineage into its species
    lineage,  a  parsimony  strategy  illustrated  by  cladograms  con-
    structed from globin sequences. Syst. Zool., 28, 132-168
  • Roderic Guigo, Ilya Muchnik, Temple F. Smith (1996) Reconstruction of Ancient Molecular Phylogeny. Molecular Phylogenetics and Evolution, Volume 6, Issue 2, October 1996, Pages 189-213

Rooting gene trees by minimizing duplications & more background on sequence function prediction:

Mathematical background:

Non-binary species trees:

Other approaches for duplication inference:

  • Chen,K., Durand,D. and Farach-Colton,M. (2000) Notung: dating gene duplications using gene family trees.  In Proceedings of the Fourth Annual International Conference on Computational Molecular Biology on RECOMB 2000,  pp. 96-106
  • Page,R.D.M. (1998) GeneTree: comparing gene and species phylo-genies using reconciled trees. Bioinformatics, 14, 819-820.
  • Page,R.D.M. and Charleston,M.A. (1997) Reconciled trees and in-congruent gene and species trees. In Mirkin,B., McMorris,F.R., Roberts,F.S. and Rzhetsky,A. (eds),  Mathematical Hierarchies in Biology, DIMACS Series in Discrete Mathematics and Theo-retical Computer Science, vol. 37, American Mathematical Society, Providence, RI, pp. 57-70.