Pipeline: tRNA identification and characterization
Workflow
_1_ acquire/access data
_2_ detect tRNAs in data
_3_ assign Operational Taxonomy Units (OTG for each tRNA)
_4_ determine MFE (free energy for each tRNA)
_5_ create output file (for each tRNA)
DETAILS
_1_ acquire/access data
_Sources
__genome
__Biosample
__Bioproject
__GSS
_Question
__How to access data source (local versus NCBI server)
_2_ detect tRNAs in data
_tRNAscan – http://lowelab.ucsc.edu/tRNAscan-SE
_3_ assign Operational Taxonomy Units (OTG for each tRNA)
_How are OTGs assigned?
__QIIME: http://qiime.org/scripts/assign_taxonomy.html
____http://www.wernerlab.org/teaching/qiime/overview/c
__PECBO: http://www.epa.gov/caddis/pecbo_intro1.html
___http://www.epa.gov/caddis/pecbo_models4.html
_4_ determine MFE (free energy for each tRNA)
Programs alternatives
__Vienna package – RNALfold: http://www.tbi.univie.ac.at/RNA/
__mfold: http://mfold.rna.albany.edu//?q=mfold/download-mfold
_5_ create output file (for each tRNA)
__origin: dataset information (1_NCBI)
__sequence (2_tRNAscan)
__assumed codon (2_tRNAscan)
__assigned OTU (4_??)
__binding energy (ViennaPackage/mFold)
References:
- tRNA-based phylogenies: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2905747/
- OTU: http://www.epa.gov/caddis/pecbo_models4.html
- RNAVienna package: http://www.almob.org/content/pdf/1748-7188-6-26.pdf