Alignment Uncertainty and Genomic Analysis

by: Karen M Wong, Marc A Suchard, John P Huelsenbeck

Science, Vol. 319, No. 5862. (25 January 2008), pp. 473-476.

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The statistical methods applied to the analysis of genomic data do not account for uncertainty in the sequence alignment. Indeed, the alignment is treated as an observation, and all of the subsequent inferences depend on the alignment being correct. This may not have been too problematic for many phylogenetic studies, in which the gene is carefully chosen for, among other things, ease of alignment. However, in a comparative genomics study, the same statistical methods are applied repeatedly on thousands of genes, many of which will be difficult to align. Using genomic data from seven yeast species, we show that uncertainty in the alignment can lead to several problems, including different alignment methods resulting in different conclusions. 10.1126/science.1151532

@article{citeulike:2288308, abstract = {The statistical methods applied to the analysis of genomic data do not account for uncertainty in the sequence alignment. Indeed, the alignment is treated as an observation, and all of the subsequent inferences depend on the alignment being correct. This may not have been too problematic for many phylogenetic studies, in which the gene is carefully chosen for, among other things, ease of alignment. However, in a comparative genomics study, the same statistical methods are applied repeatedly on thousands of genes, many of which will be difficult to align. Using genomic data from seven yeast species, we show that uncertainty in the alignment can lead to several problems, including different alignment methods resulting in different conclusions. 10.1126/science.1151532}, author = {Wong, Karen M. and Suchard, Marc A. and Huelsenbeck, John P. }, citeulike-article-id = {2288308}, doi = {http://dx.doi.org/10.1126/science.1151532}, journal = {Science}, keywords = {bioinformatics, genomics}, month = {January}, number = {5862}, pages = {473--476}, posted-at = {2008-05-20 17:52:18}, priority = {2}, title = {Alignment Uncertainty and Genomic Analysis}, url = {http://dx.doi.org/10.1126/science.1151532}, volume = {319}, year = {2008} }

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TY - JOUR ID - citeulike:2288308 L3 - citeulike-article-id:2288308 TI - Alignment Uncertainty and Genomic Analysis JF - Science VL - 319 IS - 5862 SP - 473 EP - 476 N2 - The statistical methods applied to the analysis of genomic data do not account for uncertainty in the sequence alignment. Indeed, the alignment is treated as an observation, and all of the subsequent inferences depend on the alignment being correct. This may not have been too problematic for many phylogenetic studies, in which the gene is carefully chosen for, among other things, ease of alignment. However, in a comparative genomics study, the same statistical methods are applied repeatedly on thousands of genes, many of which will be difficult to align. Using genomic data from seven yeast species, we show that uncertainty in the alignment can lead to several problems, including different alignment methods resulting in different conclusions. 10.1126/science.1151532 KW - bioinformatics KW - genomics AU - Wong, Karen AU - Suchard, Marc AU - Huelsenbeck, John PY - 2008/01/25/ UR - http://dx.doi.org/10.1126/science.1151532 ER -

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