The findMiRNA and precExtract Software Source code for both programs findMiRNA and precExtract are available for download (updated for Fedora core 4). They were developed and tested under Red Hat Linux 9, with the GNU C++ compiler version 3.X. You may have problems with other compilers. All source code files fall under the terms of the GNU General Public License. By downloading the source code you agree to the terms of that license. You will need the Vienna RNA Package in order to compile this software. You can retrieve the source code from the original site, or as an RPM from BioLinux. Updates: 1/13/2005 Some cosmetic and organizational changes to the source code, and incorporation of another supplemental program, hashedPrecExtract. No changes to functionality were made so results should be identical. Whole Genome Scan findmirna_results.gz - (2.1Gb Uncompressed) - All predictions for the entire Arabidopsis thaliana genome. There is also a README explaining the findMiRNA output format. The raw data is available in a gzipped format (uncompress with gzip). Exploratory Scan - Ranked Clusters 1599.ranked_clusters.gz - The 1599 ranked clusters generated from the exploratory scan of 5701 transcripts. Potential precursor sequences that were predicted to target the same region of a transcript and had candidate miRNA sequences on the same arm of the hairpin were grouped into sequence families. These sequence families were ranked using a formula that takes advantage of the characteristic pattern of sequence conservation observed for miRNA precursor families in which the miRNA/miRNA* regions are more conserved than the interstice (region between miRNA/miRNA* sequences). Known miRNA precursor families were shown to be enriched towards the top of these ranked clusters.
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