Rosenbloom Kate, Taylor James, Schaeffer Stephen, Kent Jim, Haussler David, Miller Webb
Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA.
Methods Mol Biol. 2008;422:133-44. doi: 10.1007/978-1-59745-581-7_9.
The UC Santa Cruz Genome Browser provides a number of resources that can be used for phylogenomic studies, including (1) whole-genome sequence data from a number of vertebrate species, (2) pairwise alignments of the human genome sequence to a number of other vertebrate genome, (3) a simultaneous alignment of 17 vertebrate genomes (most of them incompletely sequenced) that covers all of the human sequence, (4) several independent sets of multiple alignments covering 1% of the human genome (ENCODE regions), (5) extensive sequence annotation for interpreting those sequences and alignments, and (6) sequence, alignments, and annotations from certain other species, including an alignment of nine insect genomes. We illustrate the use of these resources in the context of assigning rare genomic changes to the branch of the phylogenetic tree where they appear to have occurred, or of looking for evidence supporting a particular possible tree topology. Sample source code for performing such studies is available.
加州大学圣克鲁兹分校基因组浏览器提供了许多可用于系统发育基因组学研究的资源，包括：（1）来自多个脊椎动物物种的全基因组序列数据；（2）人类基因组序列与其他多个脊椎动物基因组的成对比对；（3）覆盖所有人类序列的17个脊椎动物基因组（其中大多数测序不完整）的同步比对；（4）覆盖人类基因组1%（ENCODE区域）的几个独立的多重比对数据集；（5）用于解释这些序列和比对的广泛序列注释；以及（6）来自某些其他物种的序列、比对和注释，包括九个昆虫基因组的比对。我们举例说明了如何利用这些资源来确定罕见基因组变化出现在系统发育树的哪个分支上，或者寻找支持特定可能树拓扑结构的证据。执行此类研究的示例源代码是可用的。
