G4CatchAll

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Minimum G-tract length allowed: Minimum G-tract length allowed



Loop limits for GQs with (+3)-guanine-tracts: Defines limits of loops for G-quadruplexes with 3 or more-guanines-long Gtracts

min max


Loop limits for GQs with (2)-guanine-tracts: Defines limits of loops for G-quadruplexes with 2-guanines-long Gtracts

min max

Extreme loop: Defines the minimum G-tract length for permission of an extreme loop.



Extreme loop limits: An extreme loop allows a single loop to have longer or shorter than typical loop limits set above."

min max

Imperfect G-tracts allowed: Defines the number of atypical or "imperfect" G-tracts allowed for G-quadruplexes with G-tracts of at least 3 guanines.



Type of imperfect G-tracts: Defines the nature of the imperfect G-tracts allowed. Bulges are G-tracts with bulding nucleotides, while mismatches are G-tracts missing a single guanine.


Check both strands: By default the program searches both strands by reversing the regex. If used only the given strand is searched for matches.



Include flanking nucleotides: By default the program extracts only matching sequences. If used flanking nucleotides are also included in the search. Please note if used G-quadruplex-forming sequences at the beginning or ending of the sequences may be missed. Consider adding "N" to the edges of the sequence if G-quadruplex forming sequences are expected to be found at the very edge of the target sequence.



Merge overlapping G-quadruplex on same strand: Putative G-quadruplex-forming sequences may be found overlapping on the same strand. It is recommended to merge since not merging may result in huge number of matches and cause memory issues



Maximum length allowed for a G-guadruplex: not including overlapping G-quadruplexes

max

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Please cite
Doluca, O. (2019). G4Catchall: A G-quadruplex prediction approach considering atypical features. Journal Of Theoretical Biology, 463, 92-98. doi: 10.1016/j.jtbi.2018.12.007

Website made by Tugay Direk. The algorithm was developed by Osman Doluca. This work was supported by TUBITAK, project no 216S854.