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» Sequence alignment with tandem duplication
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ISBRA
2009
Springer
14 years 2 months ago
Prediction of Contiguous Regions in the Amniote Ancestral Genome
Abstract. We investigate the problem of inferring contiguous ancestral regions (CARs) of the genome of the last common ancestor of all extant amniotes, based on the currently seque...
Aïda Ouangraoua, Frédéric Boyer...
BMCBI
2006
100views more  BMCBI 2006»
13 years 7 months ago
DNPTrapper: an assembly editing tool for finishing and analysis of complex repeat regions
Background: Many genome projects are left unfinished due to complex, repeated regions. Finishing is the most time consuming step in sequencing and current finishing tools are not ...
Erik Arner, Martti T. Tammi, Anh-Nhi Tran, Ellen K...
BMCBI
2005
108views more  BMCBI 2005»
13 years 7 months ago
SplitTester: software to identify domains responsible for functional divergence in protein family
Background: Many protein families have undergone functional divergence after gene duplications such that current subgroups of the family carry out overlapping but distinct biologi...
Xiang Gao, Kent Vander Velden, Daniel F. Voytas, X...
BMCBI
2007
162views more  BMCBI 2007»
13 years 8 months ago
Three-Dimensional Phylogeny Explorer: Distinguishing paralogs, lateral transfer, and violation of "molecular clock" assumption w
Background: Construction and interpretation of phylogenetic trees has been a major research topic for understanding the evolution of genes. Increases in sequence data and complexi...
Namshin Kim, Christopher Lee
BMCBI
2008
131views more  BMCBI 2008»
13 years 8 months ago
CoCoNUT: an efficient system for the comparison and analysis of genomes
Background: Comparative genomics is the analysis and comparison of genomes from different species. This area of research is driven by the large number of sequenced genomes and hea...
Mohamed Ibrahim Abouelhoda, Stefan Kurtz, Enno Ohl...