Lirex： A Package for Identification of LongInverted Repeats in Genomes  

作　　者：Yong Wang Jiao-Mei Huang 

机构地区：[1]Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China

出　　处：《Genomics, Proteomics & Bioinformatics》2017年第2期141-146,共6页基因组蛋白质组与生物信息学报（英文版）

基　　金：supported by the National Natural Science Foundation of China (Grant Nos. 41476104 and 31460001);the Strategic Priority Research Program of the Chinese Academy of Sciences (Grant No. XDB06010201);the International Science and Technology Cooperation Project of Hainan Province, China (Grant No. KJHZ2015-22);the support from the Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences (Grant Nos. SIDSSE-BR-201303 and SIDSSE-201305)

摘　　要：Long inverted repeats(LIRs) are evolutionarily and functionally important structures in genomes because of their involvement in RNA interference, DNA recombination, and gene duplication. Identification of LIRs is highly complicated when mismatches and indels between the repeats are permitted. Long inverted repeat explorer(Lirex) was developed and introduced in this report. Written in Java, Lirex provides a user-friendly interface and allows users to specify LIR searching criteria, such as length of the region, as well as pattern and size of the repeats. Recombinogenic LIRs can be selected on the basis of mismatch rate and internal spacer size from identified LIRs. Lirex, as a cross-platform tool to identify LIRs in a genome, may assist in designing following experiments to explore the function of LIRs. Our tool can identify more LIRs than other LIR searching tools. Lirex is publicly available at http://124.16.219.129/Lirex.Long inverted repeats(LIRs) are evolutionarily and functionally important structures in genomes because of their involvement in RNA interference, DNA recombination, and gene duplication. Identification of LIRs is highly complicated when mismatches and indels between the repeats are permitted. Long inverted repeat explorer(Lirex) was developed and introduced in this report. Written in Java, Lirex provides a user-friendly interface and allows users to specify LIR searching criteria, such as length of the region, as well as pattern and size of the repeats. Recombinogenic LIRs can be selected on the basis of mismatch rate and internal spacer size from identified LIRs. Lirex, as a cross-platform tool to identify LIRs in a genome, may assist in designing following experiments to explore the function of LIRs. Our tool can identify more LIRs than other LIR searching tools. Lirex is publicly available at http://124.16.219.129/Lirex.

关 键 词：Lirex Inverted repeats Recombination STEM-LOOP Mismatch rate 

分 类 号：Q78[生物学—分子生物学]