Abstract
The problem of predicting non-long terminal repeats (LTR) like long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs) from the DNA sequence is still an open problem in bioinformatics. To elevate the quality of annotations of LINES and SINEs an automated tool "RetroPred" was developed. The pipeline allowed rapid and thorough annotation of non-LTR retrotransposons. The non-LTR retrotransposable elements were initially predicted by Pairwise Aligner for Long Sequences (PALS) and Parsimonious Inference of a Library of Elementary Repeats (PILER). Predicted non-LTR elements were automatically classified into LINEs and SINEs using ANN based on the position specific probability matrix (PSPM) generated by Multiple EM for Motif Elicitation (MEME). The ANN model revealed a superior model (accuracy = 78.79 +/- 6.86 %, Q(pred) = 74.734 +/- 17.08 %, sensitivity = 84.48 +/- 6.73 %, specificity = 77.13 +/- 13.39 %) using four-fold cross validation. As proof of principle, we have thoroughly annotated the location of LINEs and SINEs in rice and Arabidopsis genome using the tool and is proved to be very useful with good accuracy. Our tool is accessible at http://www.juit.ac.in/RepeatPred/home.html.
Highlights
Long interspersed elements (LINEs) and short interspersed elements (SINEs) are non-long terminal repeats (LTR) retrotransposons that reside within cells of a host organism, copying and inserting themselves into the host genome
Repetitive sequences are an important feature of eukaryotic genomes accounting for a large proportion of the genome; at least 50% of the human [1] and about 80% in some plants [2] genome seems to be composed by repetitive elements
The ANN model develop in this study (200-7-2) is trained with the position specific probability matrix (PSPM) matrix calculated using Multiple EM for Motif Elicitation (MEME)
Summary
Long interspersed elements (LINEs) and short interspersed elements (SINEs) are non-LTR retrotransposons that reside within cells of a host organism, copying and inserting themselves into the host genome. The annotation of genomic repeats, typically relies on the results of a single computational program, RepeatMasker
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