jPREdictor 1.2.3

jPREdictor is used for defining motifs, searching them on sequences, weighting motifs using training sets and scoring sequences using the weighted motifs.
Short sequence fragments, namely transcription factor binding sites, are known to be enriched and clustered in such elements. These binding sites are represented as motifs and for the prediction, they must be known.
Using these motifs, it is possible to weight them by applying a positive or negative training set (model or background, respectively), to search them on sequences, and to score a sequence.
Gene regulation is the process through which an organism effects spatial and temporal differences in gene expression levels. Knowledge of cis-regulatory elements as key players in gene regulation is indispensable for the understanding of the latter and of the development of organisms.
The prediction is based on clusters of individual motifs and arbitrary combinations of these into multi-motifs with selectable minimal and maximal distances. Individual motifs can be of heterogenous classes, such as simple sequence motifs or position-specific scoring matrices.
Cluster scores are weighted occurences of multi-motifs, where the weights are derived from positive and negative training sets.

System requirements:
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Enhancements
- added the new parameter searchDirection for MultiMotifs defined via option files
- fixed an error with flat triple- and higher-order motifs reporting to few hits; this error occured rarely but regulary and did not occur for DoubleMotifs or non-flat composite-motifs consising of Double- motifs, such as (Pho-DSP1)-(Pho-DSP1)