Hi to all, I have 454 RNA transcripts assembled into Isotigs using Newbler. They are complete, they miss 5' end, they miss 3' end and sometimes they miss both (as revealed by blastx). I want only the CDS (coding sequence) because I want to check the propensity of GC (only in CDS) & hydrophilic amino acids (after translation) in my transcriptome. So do you guys know any tool which does this? So all kind of suggestions are welcome!
thank u raghul
Just to note that by definition, an incomplete transcript cannot yield a CDS. I suppose it can yield a "partial CDS".
I am having the assembled transcripts.
Thanks to all for answering the questions. I think for protein sequence analysis, I can use OrfPredictor. It takes sequences & blastx output for analysis & give predicted peptide sequences in the FASTA formatI am looking ways to identify (partial)CDS in RNA. This answer was available for another question in Biostar forum for a different question.
Thanks to all for answering the questions. I think for protein sequence analysis, I can use OrfPredictor. It takes sequences & blastx output for analysis & give predicted peptide sequences in the FASTA format. Now I am looking ways to identify (partial)CDS in RNA. This answer was available for another question in Biostar forum for a different question.