Abstract
Many long noncoding RNAs (lncRNAs) can bind to DNA sequences proximal and distal to abundant genes, thereby regulating gene expression by recruiting epigenomic modification enzymes to binding sites. Because a lncRNA's target genes scattering in a genome have correlated functions, epigenetic analyses should often be genome-wide on both genome and transcriptome levels. Multiple tools have been developed for predicting lncRNA/DNA binding, but fast and accurate genome-wide prediction remains a challenge. Here we report Fasim-LongTarget (a revised version of LongTarget), compare its performance with TDF and LongTarget using the experimental data of the lncRNA MEG3, NEAT1, and MALAT1, and describe a case of genome-wide prediction. Fasim-LongTarget is as accurate as LongTarget and more accurate than TDF and is 200 times faster than LongTarget, making accurate genome-wide prediction feasible. The code is available on the Github website (https://github.com/LongTarget/Fasim-LongTarget), and the online service is available on the LongTarget website (https://lncRNA.smu.edu.cn).