BACKGROUND: As genomes evolve after speciation, gene content, coding sequence, gene expression, and splicing all diverge with time from ancestors with close relatives. A minimum evolution general method for continuous character analysis in a phylogenetic perspective is presented that allows for reconstruction of ancestral character states and for measuring along branch evolution. RESULTS: A software package for reconstruction of continuous character traits, like relative gene expression levels or alternative splice site usage data is presented and is available for download at http://www.rossnes.org/phyrex. This program was applied to a primate gene expression dataset to detect transcription factor binding sites that have undergone substitution, potentially having driven lineage-specific differences in gene expression. CONCLUSION: Systematic analysis of lineage-specific evolution is becoming the cornerstone of comparative genomics. New methods, like phyrex, extend the capabilities of comparative genomics by tracing the evolution of additional biomolecular processes.
BACKGROUND: As genomes evolve after speciation, gene content, coding sequence, gene expression, and splicing all diverge with time from ancestors with close relatives. A minimum evolution general method for continuous character analysis in a phylogenetic perspective is presented that allows for reconstruction of ancestral character states and for measuring along branch evolution. RESULTS: A software package for reconstruction of continuous character traits, like relative gene expression levels or alternative splice site usage data is presented and is available for download at http://www.rossnes.org/phyrex. This program was applied to a primate gene expression dataset to detect transcription factor binding sites that have undergone substitution, potentially having driven lineage-specific differences in gene expression. CONCLUSION: Systematic analysis of lineage-specific evolution is becoming the cornerstone of comparative genomics. New methods, like phyrex, extend the capabilities of comparative genomics by tracing the evolution of additional biomolecular processes.
Authors: Wolfgang Enard; Philipp Khaitovich; Joachim Klose; Sebastian Zöllner; Florian Heissig; Patrick Giavalisco; Kay Nieselt-Struwe; Elaine Muchmore; Ajit Varki; Rivka Ravid; Gaby M Doxiadis; Ronald E Bontrop; Svante Pääbo Journal: Science Date: 2002-04-12 Impact factor: 47.728
Authors: Christian Roth; Matthew J Betts; Pär Steffansson; Gisle Saelensminde; David A Liberles Journal: Nucleic Acids Res Date: 2005-01-01 Impact factor: 16.971
Authors: Christian Roth; Matthew J Betts; Pär Steffansson; Gisle Saelensminde; David A Liberles Journal: Nucleic Acids Res Date: 2005-01-01 Impact factor: 16.971