检测番茄BAC序列中paralogs的blastn参数研究

详细信息

Determination of Blastn Parameters for Predicting Paralogs in Tomato BAC Clones

摘要: 并系同源(paralog)和直系同源(ortholog)是物种进化过程中产生的两种基本的同源序列类型。目前判断ortholog的方法已经基本确立,而paralog的判断却还没有统一的标准。番茄全基因组测序正在进行中,利用Gen-Bank中已有的番茄BAC序列进行一系列不同参数下的比对(blastn),根据比对结果确定了paralog预测的最佳参数,分别是E值为10^-40,匹配序列长度为200bp,序列一致率为80%。这些参数值的确定为以后在番茄BAC序列中进行paralog预测提供了适用的参数。
- 基因复制 /
- 番茄 /
- 并系同源(paralog) /
- 直系同源(ortholog) /
- Blastn
Abstract: Paralogs and orthologs are two main types of the homologous sequences originated during speciation and genome evolution.Although methods of ortholog identification across species have been develo-ped,the method or parameters for paralog prediction are still uncertain especially for solanaceous species.Now whole genome sequencing of tomato is under going,parameters for paralog prediction are needed to study the evolution of tomato genome.After self-blasting of tomato BAC DNA sequences downloaded from GenBank,here we determined that E-value≤10^-40,HSPs length≥200 bp,sequence identity≥80% are the appropriate parameters or combination of parameters.
- Genome duplication /
- Tomato /
- Paralog /
- Ortholog /
- Blastn