CPAT¶
Description¶
Using RNA-seq, tens of thousands of novel transcripts and isoforms have been identified (Djebali, et al Nature, 2012 , Carbili et al, Gene & Development, 2011) The discovery of these hidden transcriptome rejuvenate the need of distinguishing coding and noncoding RNA. However, Most previous coding potential prediction methods heavily rely on alignment, either pairwise alignment to search for protein evidence or multiple alignments to calculate phylogenetic conservation score (such as CPC , PhyloCSF and RNACode ). This is because most previously identified transcripts including protein coding RNA and short, housekeeping/regulatory RNAs such as snRNAs, snoRNA and tRNA are highly conserved.
Environment Modules¶
Run module spider cpat to find out what environment modules are available for this application.
Environment Variables¶
- HPC_CPAT_DIR - installation directory
- HPC_CPAT_BIN - executable directory
Citation¶
If you publish research that uses cpat you have to cite it as follows:
Categories¶
phylogenetics