Non-B DNA Predictor

Non-B DNAs

DNA was first identified in the late 1860s by Swiss chemist Friedrich Miescher. In the decades following, other researchers revealed additional details about the DNA molecule, including its primary chemical components and the ways in which they joined with one another. These laid the foundation for the ground breaking description of the DNA by Watson and Crick in 1953. It is now known that genomic DNA is not limited to the confines of the canonical B-forming DNA duplex described by Watson and Crick, but includes other different types of secondary structures collectively termed non-B DNA structures. Non-B DNA have recently garnered much interest because of their important roles in a variety of biological processes such as DNA replication, telomere maintenance, gene expression, viral replication, immune evasion, neurological disorders and cancers.

Non-B DNA Predictor

Non-B DNA Predictor identifies non-B DNA motifs in DNA (and RNA where applicable) sequences. Non-B DNA Predictor is based on a backend R package gquad. This app is a valuable analytical tool for experimental biologists with little computational skills. The motifs that can be identified are A-phased DNA repeats, G-quadruplexes (with or without overlaps), intramolecular triplexes (with or without overlaps), slipped motifs, short tandem repeats, triplex forming oligonucleotides and Z-DNA motifs.

To carry out predictions, the user can either paste raw nucleotide sequences or upload a fasta file or provide GenBank accession numbers into the appropriate pane. Results providing information on the positions, sequence compositions and lengths of predicted motifs are generated and can be downloaded as a csv file. If more than one sequence is provided, an input ID is generated for motifs predicted from each input sequence. For G-quadruplexes, slipped motifs and Z-DNA motifs, the degree of likeliness for a predicted motif to be formed is computed and scored as ** (more likely) or as * (less likely). Users are advised to limit each run to a maximum of 200KB of data. For runs exceeding 200KB, users may contemplate gquad. Please note that results are not stored on our server. Should you have comments, questions or suggestions, contact the maintainer (hajoge[at]uwo.ca).

Sample sequences

Sample sequences are provided for demonstration purpose. The sequences are in three formats and has been put together in a folder (total size of 184KB), which can be downloaded from here as a zip file (57KB). "Sample.fasta" should be uploaded through the "FASTA File" tab, while "SampleGenBank.txt" and "Sample.txt" should be copied into the "GenBank Number" and the "Nucleic Acid Sequences" tab areas, respectively. Each sample file includes (1) a cloned human sequence, (2) human epidermal growth factor receptor, (3) human transketolase like 1 gene and (4) human vascular endothelial growth factor A.