Example Fold Analysis¶
This directory contains a sample analysis of Hyb-format and Vienna-format data, published in the quick Crosslinking and Sequencing of Hybrids (qCLASH) experiment described in: Gay, Lauren A., et al. “Modified cross-linking, ligation, and sequencing of hybrids (qCLASH) identifies Kaposi’s Sarcoma-associated herpesvirus microRNA targets in endothelial cells.” Journal of virology 92.8 (2018): e02138-17.
This analysis investigates the folding pattern of miRNA from an experimental replicate infected with Kaposi’s Sarcoma-Associated Herpesvirus (KSHV), which are given the type name “KSHV-miRNA”. Data from the predicted folding pattern for each hybrid record produced by the “Hyb” program are analyzed, and the folds of each KSHV miRNA with a non-miRNA target are characterized to determine the per-base folding patterns.
Hybrid sequence information created by the Hyb program and the fold output are provided with the hybkit package in the databases directory, created by downstream analysis of files available at NCBI Gene Expression Ombnibus (GEO) GSE101978, at:
The data files can be copied and uncompressed by using the command:
$ sh ./prepare_data.sh
The unpacked data-files require ~150 MB of space. The completed output of the analysis requires ~30 MB of space.