This is the Linux app named CPAT whose latest release can be downloaded as prebuilt_models.zip. It can be run online in the free hosting provider OnWorks for workstations.
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CPAT
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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. While still very useful, these approaches have several limitations:
Most lncRNAs are less conserved and tend to be lineage specific which greatly limit the discrimination power of alignment-based methods. For example, of 550 lncRNAs detected from zebrafish, only 29 of them had detectable sequence
Audience
Science/Research
User interface
Web-based, Command-line
Programming Language
Python
Categories
This is an application that can also be fetched from https://sourceforge.net/projects/rna-cpat/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.
