This release changes the format of the "Results.txt" file to make it easier to parse .. it removes colon-delimited information fields from DicerCall and from the phasing results. It also adds an option to suppress phasing analysis altogether if the user so desires.
Minor change in new ShortStack.pl package in this release -- now includes a third helper script, "miR_homologs.pl". miR_homologs.pl takes as input alignments of known mature miRNAs against a reference genome, and analyzes hairpin structure and miRNA/miRNA* pairing to determine if the locus appears to conform the Meyers et al. criteria for MIRNA annotation (in the absence of expression data). It can be used in at least two ways:
1. Annotating a new genome based on miRNAs known from other species, in the absence of any small RNA expression.
2. Prefiltering entries from miRBase to a subset of loci whose predicted structures conform to accepted criteria.
Importantly, the results for miR_homologs.pl can be fed into ShortStack in --count mode, in order to compare MIRNA loci identified by homology to actual expression data.
-- THIS WEBSITE HAS BEEN REPLACED ... please go to http://sites.psu.edu/axtell for the current Axtell Lab Website! --
Michael Axtell, lab PI