PDF(Sci-hub)
Abstract：
Transposable elements (TEs) have the ability to alter individual genomic landscapes and shape the course of evolution for species in which they reside. Such profound changes can be understood by studying the biology of the organism and the interplay of the TEs it hosts. Characterizing and curating TEs across a wide range of species is a fundamental first step in this endeavor. This protocol employs techniques honed while developing TE libraries for a wide range of organisms and specifically addresses: (1) the extension of truncated de novo results into full-length TE families; (2) the iterative refinement of TE multiple sequence alignments; and (3) the use of alignment visualization to assess model completeness and subfamily structure. © 2021 Wiley Periodicals LLC. Basic Protocol: Extension and edge polishing of consensi and seed alignments derived from de novo repeat finders Support Protocol: Generating seed alignments using a library of consensi and a genome assembly.
摘要：
转座因子（TE）具有改变个体基因组景观并塑造其所在物种进化过程的能力。通过研究生物体的生物学及其宿主的相互作用，可以理解这种深刻的变化。在广泛的物种中表征和策划TE是这一努力的基本第一步。该协议采用了在开发各种生物体的TE文库时磨练的技术，具体解决了：（1）将截短的从头结果扩展到全长TE家族;（2）TE多序列比对的迭代细化;（3）使用比对可视化来评估模型完整性和亚家族结构。©2021威利期刊有限责任公司。基本方案：从头重复查找器衍生的consensi和种子比对的扩展和边缘抛光支持方案：使用consensi文库和基因组组装生成种子比对。
