Question: Processing of sequences for CodonW use
0
gravatar for majeedaasim
4 days ago by
majeedaasim20
United States
majeedaasim20 wrote:

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

codonw codin usage bias • 106 views
ADD COMMENTlink modified 3 days ago by h.mon10k • written 4 days ago by majeedaasim20

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

ADD REPLYlink written 4 days ago by h.mon10k

I have a denovo assembled transcriptome

ADD REPLYlink written 3 days ago by majeedaasim20
0
gravatar for h.mon
3 days ago by
h.mon10k
Brazil
h.mon10k wrote:

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.

ADD COMMENTlink modified 3 days ago • written 3 days ago by h.mon10k

Thanks a lot for help

ADD REPLYlink written 3 days ago by majeedaasim20
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