Question: How to obtain Coding sequence from Genomic sequence?
gravatar for MAPK
4.7 years ago by
United States
MAPK1.4k wrote:

Hi Guys,

I have some assembled genomic sequences and I know the exact frames I need to translate to obtain coding sequence and putative protein sequences, but I do not know exactly where to chop the translated frame and hence the coding region and splice sites for intron and exon boundaries. Is there a way to get coding region from given frames? Please share your knowledge.

Thank you!

coding genome • 1.4k views
ADD COMMENTlink modified 4.5 years ago by Manvendra Singh2.0k • written 4.7 years ago by MAPK1.4k

Please show what you have; if you know the exact frame, then that's where to cut!

ADD REPLYlink written 4.7 years ago by karl.stamm3.4k

Thank you for your reply, Karl. When I say assembled the genomic sequences are still unannotated and there are multiple scaffolds. Suppose I have three scaffolds for any particular protein coding gene and if I have to translate the scaffolds in two different frames each. After merging all the translated frames, I will have an unreasonably long peptide sequence/coding region. That is because the frame gets translated further beyond the 'GT' and 'AG' boundary and hence includes the non-coding regions as well. In this case I think I need to have transcriptomic sequences to unambiguously infer the coding regions. Please clarify if otherwise. Thanks again! 

ADD REPLYlink modified 4.7 years ago • written 4.7 years ago by MAPK1.4k
gravatar for Manvendra Singh
4.5 years ago by
Manvendra Singh2.0k
Berlin, Germany
Manvendra Singh2.0k wrote:

There is an easy ways to do it .

Its Coding Potential Calculator (CPC).

It takes input as fasta sequence.

Once you submit your fasta file, you get CP score for each sequences. >1 is potential protein coding and < -1 is potential non-coding RNA

CPC can reliably discriminate the coding and non-coding transcripts in ~98% accuracy.

ADD COMMENTlink written 4.5 years ago by Manvendra Singh2.0k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1408 users visited in the last hour