HALPER facilitates the identification of regulatory element orthologs across species.
HALPER facilitates the identification of regulatory element orthologs across species.
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HALPER 有助于识别跨物种的调控元件直系同源物。
DOI：
10.1093/bioinformatics/btaa493
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发表时间：
2020
期刊：
影响因子：
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通讯作者：
Pfenning,AndreasR
中科院分区：
文献类型：
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作者：
Zhang,Xiaoyu;Kaplow,IreneM;Wirthlin,Morgan;Park,TaeYoon;Pfenning,AndreasR
摘要通过基因组序列的顺式调控变化进化出多种性状，这些变化影响基因表达的幅度、时间和细胞类型特异性。高通量测序和调控基因组学的进步已经导致了单个物种中调控元件的识别，但这些基因组区域仍然难以跨分类顺序对齐，因为它们相对于蛋白质编码基因缺乏序列保守性。最近数百个基因组的组装、这些基因组的无参考 Cactus 多序列比对的生成以及用于绘制这些比对区域的 halLiftover 工具的开发，为追踪调控元件的进化提供了基础。我们提出了用于调控元件进化的 halLiftover 后处理 (HALPER)，这是一种从 halLiftover 的输出构建连续调控元件直向同源物的工具。我们预计该工具将使用户能够有效地识别数百个物种的调控元件的直系同源物，从而为通过基因表达进化的性状进化提供新的见解。可用性和实现HALPER在Python中实现并在github上提供：https://github.com/pfenninglab/halLiftover-postprocessing。补充信息补充数据可在Bioinformaticsonline获得。
SummaryDiverse traits have evolved throughcis-regulatory changes in genome sequence that influence the magnitude, timing and cell type-specificity of gene expression. Advances in high-throughput sequencing and regulatory genomics have led to the identification of regulatory elements in individual species, but these genomic regions remain difficult to align across taxonomic orders due to their lack of sequence conservation relative to protein coding genes. The groundwork for tracing the evolution of regulatory elements is provided by the recent assembly of hundreds of genomes, the generation of reference-free Cactus multiple sequence alignments of these genomes, and the development of the halLiftover tool for mapping regions across these alignments. We present halLiftover Post-processing for the Evolution of Regulatory Elements (HALPER), a tool for constructing contiguous regulatory element orthologs from the outputs of halLiftover. We anticipate that this tool will enable users to efficiently identify orthologs of regulatory elements across hundreds of species, providing novel insights into the evolution of traits that have evolved through gene expression.Availability and implementationHALPER is implemented in python and available on github: https://github.com/pfenninglab/halLiftover-postprocessing.Supplementary informationSupplementary data are available atBioinformaticsonline.