Lirex: A Package for Identification of Long Inverted Repeats in Genomes

Wang, Yong; Huang, Junzhe

doi:10.1016/j.gpb.2017.01.005

Cited by 4 publications

(3 citation statements)

References 14 publications

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“…Interestingly, they found that, in multiple cases, palindromes which happen to be near genes involved in breast carcinogenesis were among those which differed the most in cancer compared to normal cell genomes. Additionally, several other groups worked on palindrome-counting algorithms which are publicly available [ 78 , 79 ]. Moreover, efforts are being made to overcome other obstacles in identifying DNA palindromes in genomes.…”

Section: Dna Palindromes In the Human Genomementioning

confidence: 99%

Palindromes in DNA—A Risk for Genome Stability and Implications in Cancer

Miklenić

Svetec

2021

IJMS

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A palindrome in DNA consists of two closely spaced or adjacent inverted repeats. Certain palindromes have important biological functions as parts of various cis-acting elements and protein binding sites. However, many palindromes are known as fragile sites in the genome, sites prone to chromosome breakage which can lead to various genetic rearrangements or even cell death. The ability of certain palindromes to initiate genetic recombination lies in their ability to form secondary structures in DNA which can cause replication stalling and double-strand breaks. Given their recombinogenic nature, it is not surprising that palindromes in the human genome are involved in genetic rearrangements in cancer cells as well as other known recurrent translocations and deletions associated with certain syndromes in humans. Here, we bring an overview of current understanding and knowledge on molecular mechanisms of palindrome recombinogenicity and discuss possible implications of DNA palindromes in carcinogenesis. Furthermore, we overview the data on known palindromic sequences in the human genome and efforts to estimate their number and distribution, as well as underlying mechanisms of genetic rearrangements specific palindromic sequences cause.

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Section: Dna Palindromes In the Human Genomementioning

confidence: 99%

Palindromes in DNA—A Risk for Genome Stability and Implications in Cancer

Miklenić

Svetec

2021

IJMS

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“…We tested several tools including detectIR ( 25 ), findIR ( 26 ), Inverted Repeats Finder (IRF) ( 20 ) and Lirex ( 27 ) to identify LIRs, and found that IRF is the only tool that was able to identify LIRs with imperfectly matched arms longer than 600 bp. On the contrary, detectIR and findIR were used to identify inverted repeats shorter than 100 nt, developed based on the commercial software MATLAB ( 25 , 26 ).…”

Section: Data Collection and Methodsmentioning

confidence: 99%

“…On the contrary, detectIR and findIR were used to identify inverted repeats shorter than 100 nt, developed based on the commercial software MATLAB ( 25 , 26 ). Lirex was able to identify LIRs with long internal loops, but failed to identify LIRs with long arms harboring multiple mismatches and indels between each other ( 27 ). In reality, growing evidence shows that the 3.1-kb LIR reported in Drosophila ( 5 ) as well as the 15 012-bp and 3013-bp LIRs reported in rice ( 10 ) can only be identified by IRF.…”

Section: Data Collection and Methodsmentioning

confidence: 99%

LIRBase: a comprehensive database of long inverted repeats in eukaryotic genomes

Lee

Huang

et al. 2021

Nucleic Acids Research

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Small RNAs (sRNAs) constitute a large portion of functional elements in eukaryotic genomes. Long inverted repeats (LIRs) can be transcribed into long hairpin RNAs (hpRNAs), which can further be processed into small interfering RNAs (siRNAs) with vital biological roles. In this study, we systematically identified a total of 6 619 473 LIRs in 424 eukaryotic genomes and developed LIRBase (https://venyao.xyz/lirbase/), a specialized database of LIRs across different eukaryotic genomes aiming to facilitate the annotation and identification of LIRs encoding long hpRNAs and siRNAs. LIRBase houses a comprehensive collection of LIRs identified in a wide range of eukaryotic genomes. In addition, LIRBase not only allows users to browse and search the identified LIRs in any eukaryotic genome(s) of interest available in GenBank, but also provides friendly web functionalities to facilitate users to identify LIRs in user-uploaded sequences, align sRNA sequencing data to LIRs, perform differential expression analysis of LIRs, predict mRNA targets for LIR-derived siRNAs, and visualize the secondary structure of candidate long hpRNAs encoded by LIRs. As demonstrated by two case studies, collectively, LIRBase bears the great utility for systematic investigation and characterization of LIRs and functional exploration of potential roles of LIRs and their derived siRNAs in diverse species.

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Finding and Characterizing Repeats in Plant Genomes

Nicolas

Tempel

Cherif

2022

Plant Bioinformatics

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Plant genomes contain a particularly high proportion of repeated structures of various types. This chapter proposes a guided tour of available software that can help biologists to look for these repeats and check some hypothetical models intended to the large--scale search of these structures. Indeed, it may be hard to keep up with the profusion of proposals in this dynamic field and the rest of the chapter is devoted to the foundations of the search for repeats and more complex patterns. The second section introduces the key concepts that are useful for understanding the current state of the art in playing with words, applied to genomic sequences. This can be seen as the first stage of a very general approach called linguistic analysis that is interested in the analysis of natural or artificial texts. Words, the lexical level, correspond to simple repeated entities in texts or strings. In fact, biologists need to represent more complex entities where a repeat family is built on more abstract structures, including direct or inverted small repeats, motifs, composition constraints as well as ordering and distance constraints between these elementary blocks. In terms of linguistics, this corresponds to the syntactic level of a language. The last section introduces concepts and practical tools that can be used to reach this syntactic level in biological sequence analysis.

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Lirex: A Package for Identification of Long Inverted Repeats in Genomes

Cited by 4 publications

References 14 publications

Palindromes in DNA—A Risk for Genome Stability and Implications in Cancer

Palindromes in DNA—A Risk for Genome Stability and Implications in Cancer

LIRBase: a comprehensive database of long inverted repeats in eukaryotic genomes

Finding and Characterizing Repeats in Plant Genomes

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