title: SINE_scan: an efficient tool to discover short interspersed nuclear elements (SINEs) in large-scale genomic datasets.
abstract: Short Interspersed Nuclear Elements (SINEs) are transposable elements (TEs) that amplify through a copy-and-paste mode via RNA intermediates. The computational identification of new SINEs are challenging because of their weak structural signals and rapid diversification in sequences.
  
  
  
  Here we report SINE_Scan, a highly efficient program to predict SINE elements in genomic DNA sequences. SINE_Scan integrates hallmark of SINE transposition, copy number and structural signals to identify a SINE element. SINE_Scan outperforms the previously published de novo SINE discovery program. It shows high sensitivity and specificity in 19 plant and animal genome assemblies, of which sizes vary from 120 Mb to 3.5 Gb. It identifies numerous new families and substantially increases the estimation of the abundance of SINEs in these genomes.
  
  
  
  The code of SINE_Scan is freely available at http://github.com/maohlzj/SINE_Scan , implemented in PERL and supported on Linux.
  
  
  
  wangh8@fudan.edu.cn.
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: T-Life Research Center, Department of Physics, Fudan University, Shanghai 200433, People's Republic of China.
authors.forename: Hongliang
authors.initials: H
authors.lastname: Mao
authors.affiliation: T-Life Research Center, Department of Physics, Fudan University, Shanghai 200433, People's Republic of China.|Department of Genetics, University of Georgia, Athens, GA 30602, USA.
authors.forename: Hao
authors.initials: H
authors.lastname: Wang
mesh_terms: D000818:Animals; D004251:DNA Transposable Elements; D023281:Genomics / Q000379:methods*; D006801:Humans; D010944:Plants / Q000235:genetics; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods*; D020086:Short Interspersed Nucleotide Elements; D012984:Software
chemical_list: D004251:DNA Transposable Elements