1. Input DNA Sequence

2. Input LncRNA Sequence

3. Select a base piring rule set
4. Set up parameters
eq 
eq 
eq 
min
min
min
5. Draw figure
6.Shuffle sequence
7.User's email* (optional)



How and when to get results

1. A job number is generated when the job is submitted, allowing the user to retrieve and download the result. It is optional (specifically indicated by “*”) for the user to leave an email address, allowing the result to be sent to the email address automatically whenever it is finished.

2. Normally it takes about 1 hour to predict a lncRNA/DNA binding in a genomic region <= 1000000 bp, and about 3-4 days to predict a lncRNA/DNA binding in a whole genome. However, time consumption may vary, especially for genome-scale prediction, depending on the workload of the server. If no result is available after 1 day after a genomic region is chosen, or after 1 week after a whole genome is chosen, please contact us by longtarget@smu.edu.cn.

3. Be careful to choose “Shuffle DNA sequence” and “Shuffle RNA sequence”, the two functions test statistical robustness of results, are very time-consuming (100 times the normal time-consumption), and are normally unnecessary (see an example in the supplementary material of He et al. Bioinforamtics 2015, 31:178–186).

History of updates

Jan 2015 v1.0: Predicting DNA binding motifs and binding sites of a lncRNA in a genomic region <=1000000 bp in any of the 17 species.

July 2017 v2.0: Predicting DNA binding motifs and binding sites of a lncRNA in a genome-scale for humans (hg19) and mice (mm10).

Dec 2017 v2.1: Predicting DNA binding motifs and binding sites of a lncRNA in a genome-scale for all species, plus humans (hg38).

Related citations

He S, Zhang H, Liu H, Zhu H. LongTarget: a tool to predict lncRNA DNA-binding motifs and binding sites via Hoogsteen base-pairing analysis. Bioinformatics 2015, 31:178–186.

Liu H, Shang X, Zhu H. LncRNA/DNA binding analysis reveals losses and gains and lineage specificity of genomic imprinting in mammals. Bioinformatics 2017, 33:1431–1436.