TY - GEN
T1 - Aligning two genomic sequences that contain duplications
AU - Hou, Minmei
AU - Riemer, Cathy
AU - Berman, Piotr
AU - Hardison, Ross C.
AU - Miller, Webb
PY - 2009
Y1 - 2009
N2 - It is difficult to properly align genomic sequences that contain intra-species duplications. With this goal in mind, we have developed a tool, called TOAST (two-way orthologous alignment selection tool), for predicting whether two aligned regions from different species are orthologous, i.e., separated by a speciation event, as opposed to a duplication event. The advantage of restricting alignment to orthologous pairs is that they constitute the aligning regions that are most likely to share the same biological function, and most easily analyzed for evidence of selection. We evaluate TOAST on 12 human/mouse gene clusters.
AB - It is difficult to properly align genomic sequences that contain intra-species duplications. With this goal in mind, we have developed a tool, called TOAST (two-way orthologous alignment selection tool), for predicting whether two aligned regions from different species are orthologous, i.e., separated by a speciation event, as opposed to a duplication event. The advantage of restricting alignment to orthologous pairs is that they constitute the aligning regions that are most likely to share the same biological function, and most easily analyzed for evidence of selection. We evaluate TOAST on 12 human/mouse gene clusters.
UR - http://www.scopus.com/inward/record.url?scp=78651242141&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=78651242141&partnerID=8YFLogxK
U2 - 10.1007/978-3-642-04744-2_9
DO - 10.1007/978-3-642-04744-2_9
M3 - Conference contribution
AN - SCOPUS:78651242141
SN - 3642047432
SN - 9783642047435
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 98
EP - 110
BT - Comparative Genomics - International Workshop, RECOMB-CG 2009, Proceedings
T2 - 7th International Workshop on Comparative Genomics, RECOMB-CG 2009
Y2 - 27 September 2009 through 29 September 2009
ER -