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Triplex
Searches and visualizes intramolecular triplex-forming sequences in DNA. triplex provides functions for identification and visualization of potential intramolecular triplex patterns in DNA sequence. The main functionality is to detect the positions of subsequences capable of folding into an intramolecular triplex (H-DNA) in a much larger sequence. Functions producing 2D and 3D diagrams of the identified triplexes allow instant visualization of the search results. In connection with R language and existing libraries for statistical analysis, the package represents powerful tool for molecular biologists interested in analysis of non-canonical DNA structures such as triplexes.
NeSSie / Nucleic-acids elements of Sequence Symmetry identification
Searches imperfection-tolerant symmetric motifs at genome wide scale. NeSSie uses the calculation of Shannon entropy and simple linguistic complexity measures to correlate potential enrichment of identified patterns in genomic regions with a peculiar nucleotide composition. It can achieve searches of mirrors, potential triplex forming patterns and palindromes by slightly altering the implemented dynamic programming algorithm.
TDF / Triplex Domain Finder
Characterizes the triple helix forming potential of RNA and DNA regions. TDF tests whether particular RNA regions are likely to form DNA binding domains (DBD) in candidate lncRNAs and potential target DNA regions (e.g. promoters of differentially regulated genes after knockdown of the lncRNA). Moreover, DNA binding sites associated with the predicted DBDs are used to indicate potential target DNA regions, e.g. genes with high binding site coverage in their promoter. TDF provides two distinct statistical tests: (i) promoter test - used to evaluate the triple helix potential in promoters and (2) genomic region test - used to test triple helix potential in a given set of genomic regions. The command line tool provides results on a user friendly and graphical html interface.
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