title: Lirex: A Package for Identification of Long Inverted Repeats in Genomes.
abstract: 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.
authors.affiliation: Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China. Electronic address: wangy@idsse.ac.cn.
authors.forename: Yong
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China.
authors.forename: Jiao-Mei
authors.initials: JM
authors.lastname: Huang
mesh_terms: D015894:Genome, Human; D006801:Humans; D055029:Inverted Repeat Sequences; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
keywords: Inverted repeats; Lirex; Mismatch rate; Recombination; Stem-loop