Cauldron Nicholas C, Sudermann Martha A, Parada-Rojas Camilo H, Grünwald Niklaus J
Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA.
Horticultural Crops Disease and Pest Management Research Unit, United States Department of Agriculture-Agricultural Research Service, Corvallis, OR, USA.
Methods Mol Biol. 2025;2892:151-168. doi: 10.1007/978-1-0716-4330-3_11.
Pathogens have evolved effector proteins to suppress host immunity and facilitate plant infections. RxLR effectors are small, secreted effector proteins with conserved RxLR and dEER amino acid motifs at the N terminus and highly variable C termini and are commonly found in oomycete species. We provide computational approaches to annotate RxLR candidate effector genes in a genome assembly in FASTA format with an available GFF file. Hidden Markov Modeling (HHM) is used in combination with regular expressions to search for RxLR and EER amino acid patterns.
病原体已经进化出效应蛋白来抑制宿主免疫并促进植物感染。RxLR效应蛋白是一类小的分泌型效应蛋白，其N端具有保守的RxLR和dEER氨基酸基序，C端高度可变，常见于卵菌物种中。我们提供了计算方法，用于在具有可用GFF文件的FASTA格式基因组组装中注释RxLR候选效应基因。隐马尔可夫模型（HHM）与正则表达式结合使用，以搜索RxLR和EER氨基酸模式。
