PAREsnip is a fast user-friendly multi-platform bioinformatics tool to find targets of small RNAs using the degradome. A full PDF manual for PAREsnip is available here
Minimum: Java SE 6 / 6 Gb RAM Recommended: Java SE 6 / 16 Gb RAM
Choose PAREsnip from the Tools menu in the Workbench. To start the tool from the command line, navigate to the Workbench installation directory and issue the command
java -jar Workbench.jar -tool paresnip
The syntax for providing inputs to the tool will be displayed.
The PARESnip application after performing an analysis. Additional information and statistics for each of the input data sets is provided in the information area (top left box). This information includes the number of sequences and sequence length distributions. In the top-right box, shorter informational and instructional messages are provided to help guide a user through the analysis. The estimated time remaining to complete processing is also shown. Small RNA/target interactions are shown in the ‘Output’ table. The table can be sorted by clicking on a column header. The column order may be changed using drag and drop. The search box at the bottom-left can be used to search the table – partial strings are matched and case is ignored.
- Select Open to choose the input files.
- Select Save… or Save as… to save results.
- Select Reset to reinitialise PARESnip.
- ‘Close’ will close the window
- Select Start to begin processing
- Select ‘Cancel’ to stop execution.
- Select View T-plots in VisSR to visualise the results in VisSR. A T-plot for each interaction can be displayed.
A description of the columns in the result file
Gene – the ID or description of the mRNA/transcript.
Category – Potential cleavage sites on a single transcript can be categorized according to degradome read abundance. Category 0 is the strongest signal and 4 the weakest.
Cleavage Position – the position on the transcript where cleavage has been identified.
P-Value – a score that indicates how likely the reported duplex occurred by chance.
*Fragment Abundance – the abundance for the degradome fragment (tag) indicating cleavage at that position.
*Weighted Fragment Abundance – calculated by dividing the abundance of a degradome fragment (tag) by the number of positions across all transcripts to which the tag has aligned.
*Normalized Weighted Fragment Abundance – weighted Fragment abundance/total number of fragments x 1,000,000.
Duplex – the sRNA|mRNA alignment.
Alignment Score – within the duplex, a mismatch contributes 1.0 to the score, unless it is a G-U (wobble) pair in which case it contributes 0.5 to the score. A gap in the alignment contributes a value of 1.0 to the score.
Short Read ID – the ID of the sRNA.
Short Read Abundance – the abundance of the sRNA.
Normalized Short Read Abundance – sRNA abundance/total number of sRNAs x 1,000,000.