Computational reconstruction of ancestral DNA sequences. Export

@article{citeulike:3683108, abstract = {This chapter introduces the problem of ancestral sequence reconstruction: given a set of extant orthologous DNA genomic sequences (or even whole-genomes), together with a phylogenetic tree relating these sequences, predict the DNA sequence of all ancestral species in the tree. Blanchette et al. (1) have shown that for certain sets of species (in particular, for eutherian mammals), very accurate reconstruction can be obtained. We explain the main steps involved in this process, including multiple sequence alignment, insertion and deletion inference, substitution inference, and gene arrangement inference. We also describe a simulation-based procedure to assess the accuracy of the reconstructed sequences. The whole reconstruction process is illustrated using a set of mammalian sequences from the CFTR region.}, author = {Blanchette, M. and Diallo, A. B. and Green, E. D. and Miller, W. and Haussler, D.}, citeulike-article-id = {3683108}, citeulike-linkout-0 = {http://dx.doi.org/10.1007/978-1-59745-581-7_11}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/18629667}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=18629667}, doi = {10.1007/978-1-59745-581-7_11}, issn = {1064-3745}, journal = {Methods in molecular biology (Clifton, N.J.)}, keywords = {2008, accuracy, alignmnent, ancestral, multiple, phylogenetic, sequence, species, tree}, pages = {171--184}, posted-at = {2008-11-25 09:26:55}, priority = {2}, title = {Computational reconstruction of ancestral DNA sequences.}, url = {http://dx.doi.org/10.1007/978-1-59745-581-7_11}, volume = {422}, year = {2008} }

TY - JOUR ID - citeulike:3683108 L3 - citeulike-article-id:3683108 N2 - This chapter introduces the problem of ancestral sequence reconstruction: given a set of extant orthologous DNA genomic sequences (or even whole-genomes), together with a phylogenetic tree relating these sequences, predict the DNA sequence of all ancestral species in the tree. Blanchette et al. (1) have shown that for certain sets of species (in particular, for eutherian mammals), very accurate reconstruction can be obtained. We explain the main steps involved in this process, including multiple sequence alignment, insertion and deletion inference, substitution inference, and gene arrangement inference. We also describe a simulation-based procedure to assess the accuracy of the reconstructed sequences. The whole reconstruction process is illustrated using a set of mammalian sequences from the CFTR region. JF - Methods in molecular biology (Clifton, N.J.) SN - 1064-3745 EP - 184 TI - Computational reconstruction of ancestral DNA sequences. VL - 422 SP - 171 KW - 2008 KW - accuracy KW - alignmnent KW - ancestral KW - multiple KW - phylogenetic KW - sequence KW - species KW - tree AU - Blanchette, M AU - Diallo, AB AU - Green, ED AU - Miller, W AU - Haussler, D PY - 2008/// UR - http://dx.doi.org/10.1007/978-1-59745-581-7_11 ER -