CHANGES IN VERSION 1.4.x ------------------------ BUG FIXES o Fixed uninitialised variable causing slightly stochastic behaviour. o Fixed bug blocking alternative PQS with zero-length loop to be found. o Fixed inefficient looping through long non-guanine sequence regions. o Updated default scoring parameters to slightly better-performing combination. o Removed bug-prone special support for edge mismatches. o Fixed integer division to floating point division in the computation of loop length mean. CHANGES IN VERSION 1.3.x ------------------------ NEW FEATURES: o Added estimated time to complete (ETTC) to the progress line. o New default values for scoring parameters as a result from training on G4-seq experimental data and co-testing on a set of known quadruplexes from literature. o New PQS metadata reported: number of tetrads, bulges, mismatches and loop lengths. To get this data, use elementMetadata accessor function. o New algorithm option: reporting of all overlapping PQS. o Score distribution is reported. For each sequence position you get maximal score of PQS that was found overlapping the position. For details, see scoreDistribution function. o Novel scoring parameter: exponent of loop length mean in the scoring equation to express non-linear dependency of the PQS propensity to the loop lengths. BUG FIXES o Minimal loop length is set back to 0 by default, but only one zero-length loop is allowed by the scoring system. o Fixed unintentional cast of loop length mean factor and loop standard deviation factors from float to integer. CHANGES IN VERSION 1.2.x ------------------------ BUG FIXES o Minimal loop length is now set to 1 by default. o Removed linking dependency on the flowCore package. o Fixed bug responsible for a segmentation fault. Great credit belongs to Diego Andino for sending a bug report. CHANGES IN VERSION 1.0.0 ------------------------ o Novel algorithm for identification of potential intramolecular G-quadruplex (G4) patterns in DNA sequence. o Supports multiple defects in G-runs like bulges or mismatches. o Provides the most accurate results currently available. o Highly customizable to detect even novel G4 types that might be discovered in the future.