Question: How to obtain Coding sequence from Genomic sequence?
0
gravatar for MAPK
4.7 years ago by
MAPK1.4k
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
2
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).

http://cpc.cbi.pku.edu.cn/

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
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