Mercurial > repos > earlhaminst > miranda
changeset 3:ed25cd2323a7 draft default tip
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/miranda commit 457bb20f9c1c007b42d79b08527f5c558529ab8a-dirty
| author | earlhaminst |
|---|---|
| date | Mon, 24 Feb 2025 17:08:56 +0000 |
| parents | 9c8ff1bdd041 |
| children | |
| files | miranda.xml |
| diffstat | 1 files changed, 0 insertions(+), 2 deletions(-) [+] |
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--- a/miranda.xml Mon Dec 21 17:17:34 2020 +0000 +++ b/miranda.xml Mon Feb 24 17:08:56 2025 +0000 @@ -42,8 +42,6 @@ The second phase of the algorithm takes high-scoring alignments (i.e. those above the alignment score threshold) detected from phase 1 and estimates the thermodynamic stability of RNA duplexes based on these alignments. This second phase of the method utilizes folding routines from the RNAlib library, which is part of the ViennaRNA package written by Ivo Hofacker. At this stage we generate a constrained fictional single-stranded RNA composed of the query sequence, a linker and the reference sequence (reversed). This structure is then folded using RNAlib and the minimum free energy (DG kcal/mol) is calculated for that structure. Finally, detected targets with energies less than a chosen energy threshold are selected as potential target sites. Target site alignments passing both thresholds and other information is produced as output. - -View the original miRanda manual: http://cbio.mskcc.org/microrna_data/manual.html ]]></help> <citations> <citation type="doi">10.1186/gb-2003-5-1-r1</citation>