Welcome to lncRNA.smu.edu.cn !

This website currently consists of two software – LongTarget and LongMan. LongTarget was developed to predict a lncRNA’s DNA binding motifs and binding sites in a genomic region based on potential base pairing rules between a RNA sequence and a DNA duplex. We tested LongTarget using multiple human and mouse lncRNAs together with well-known genome imprinting clusters and genes with known lncRNA binding in humans and mice (He et al. LongTarget: a tool to predict lncRNA DNA-binding motifs and binding sites via Hoogsteen base-pairing analysis. Bioinformatics, 2015, 31:178–186), revealing that LongTarget can satisfactorily predict lncRNAs’ DNA binding sites. We further used LongTarget to analysis the binding of lncRNAs that control genomic imprinting in well-known imprinting regions in multiple mammals (Liu et al. LncRNA/DNA binding analysis reveals losses and gains and lineage specificity of genomic imprinting in mammals. Bioinformatics, 2017, 33:1431–1436), revealing that lncRNAs and imprinting sites show significant losses and gains and lineage-specificity, that a lncRNA may have many binding sites in a genome, and that multiple lncRNAs may bind to the same genomic sites.More

Recently, we have integrated LongTarget into LongMan, thus creating a seamless pipeline for cross-species and genome-scale lncRNA/DNA binding analysis. To facilitate genome-scale analysis, we make LongMan include the whole genome sequence of 17 mammals. Currently two kinds of genome-scale lncRNA/DNA binding analysis are available: (1) to predict the DNA binding sites of a lncRNA in promoter regions of all transcripts in any of the 17 mammals (embedded in the LongTarget section), (2) to predict the DNA binding sites of all lncRNAs in a mammalian genome in a genomic region <=20000 bp (embedded in the LongMan section). The limit of 20000 bp will be relaxed soon after our server is upgraded.

Having a plain user interface though, LongMan provides strong database search functions comparable to those in other popular lncRNA databases. To better serve the users who may frequently use other databases and want to analyze lncRNAs downloaded from elsewhere, we have developed LongTarget-BE, a variant of LongTarget for Batch lncRNA/DNA binding analysis using External data. The user can choose to submit a job with multiple lncRNA sequences and one DNA sequence, or one lncRNA sequence and multiple DNA sequences. More details about the application of the pipeline, including examples, are given in the article “Lin et al. Pipelines for cross-species and genome-wide prediction of long noncoding RNA binding. Nature Protocols, 2019, 14(3):795-818.” . Functions of this website are tested to work well with Google Chrome and Mozilla Firefox. Please send inquiries and comments to  longtarget@smu.edu.cn.

12 Oct 2019 Update: Newly annotated lncRNAs in GENCODE 32(human), GENCODE M23(mouse) and NCBI Release 109(human) were gathered into LongMan.
5 Mar 2019 Notification: Since whole-genome predictions are highly time-consuming and tasks have been densely queued, to ensure fairness, for the moment we stipulate that each user can submit at most 5 whole-genome predictions. If this quota can not meet your needs, feel free to contact zhuhao@smu.edu.cn.
4 Mar 2019 Notification: Tasks are queued, because the servers are overloaded.