Genomic features in the breakpoint regions between syntenic blocks
Genomic features in the breakpoint regions between syntenic blocks
复制标题
DOI：
10.1093/bioinformatics/bth934
复制
发表时间：
2004-08-04
期刊：
影响因子：
5.8
通讯作者：
Sankoff, David
中科院分区：
文献类型：
--
作者：
Trinh, Phil;McLysaght, Aoife;Sankoff, David
动机：基于从UCSC基因组浏览器中提取的数据，我们研究了人类和小鼠中保守的同线块之间的大部分未对齐区域。这些区域包含由反转，易位和其他processes.Results：我们建议解释有限数量的基因组对齐的断点的邻域中引起的进化断点。我们折扣的推断广泛的断点重复使用的人工制品在同线块的重建。我们发现，在断点区域的小对齐片段的数量，大小和分布依赖于相邻块和同一染色体上的其他块的起源。我们考虑到这一点，并在该地区的普遍损失的对齐部分由人工制品由于对齐协议和部分由突变过程后，重排事件的操作。这些结果与几乎在整个基因组上随机发生的断裂点一致。
Motivation: We study the largely unaligned regions between the syntenic blocks conserved in humans and mice, based on data extracted from the UCSC genome browser. These regions contain evolutionary breakpoints caused by inversion, translocation and other processes.Results: We suggest explanations for the limited amount of genomic alignment in the neighbourhoods of breakpoints. We discount inferences of extensive breakpoint reuse as artefacts introduced during the reconstruction of syntenic blocks. We find that the number, size and distribution of small aligned fragments in the breakpoint regions depend on the origin of the neighbouring blocks and the other blocks on the same chromosome. We account for this and for the generalized loss of alignment in the regions partially by artefacts due to alignment protocols and partially by mutational processes operative only after the rearrangement event. These results are consistent with breakpoints occurring randomly over virtually the entire genome.