Processing of sequences for CodonW use

Question

[majeedaasim]

I need to perform codon usage analysis. I read about CodonW and CodonO. From the literature, input sequence needs to be first checked for accuracy. The input sequence shall have 1. Shall be full length 2.No codons of transposons 3. No internal stop codons.

I require help in the sense of processing the raw sequences in following directions; 1. How to remove UTRs from entire sequences to get only coding sequences (Better tool for it). 2. CodonW has a reference set of codons belonging to few prokaryotic organisms, however, the option is to use a better personal one. Where from I shall get the codon set for my species considering it is eukaryote.

Thanks

[h.mon]

What type of data do you have? An assembled transcriptome? An annotated genome?

[majeedaasim]

I have a denovo assembled transcriptome

Answer 1

[h.mon]

If you have an assembled transcriptome, then I would suggest TransDecoder

Output files explained

[...]

longest_orfs.cds : the nucleotide coding sequence for all detected ORFs

You will need to grep the transcripts corresponding to complete predicted peptides, as it predict partial peptides as well.

Another option is GeneMarkS-T, but I don't remember for sure if it outputs the coding region of predicted transcripts.

[majeedaasim]

Thanks a lot for help