pqsfinder - Identification of potential quadruplex forming sequences
Pqsfinder detects DNA and RNA sequence patterns that are likely to fold into an intramolecular G-quadruplex (G4). Unlike many other approaches, pqsfinder is able to detect G4s folded from imperfect G-runs containing bulges or mismatches or G4s having long loops. Pqsfinder also assigns an integer score to each hit that was fitted on G4 sequencing data and corresponds to expected stability of the folded G4.
Last updated 4 months ago
motifdiscoverysequencematchinggeneregulation
2.00 score 21 dependenciestriplex - Search and visualize intramolecular triplex-forming sequences in DNA
This package 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. The potential H-DNA (triplexes) should be made of as many cannonical nucleotide triplets as possible. The package includes visualization showing the exact base-pairing in 1D, 2D or 3D.
Last updated 4 months ago
sequencematchinggeneregulation
0.09 score 19 dependencies