brianjohnhaas
commented
4 years ago Hi,
TransDecoder long orfs finds it, but as a longer 5' partial sequence that begins off the end of the contig.
Screenshot attached.
best,
~b
Closed shamsbhuiyan closed 1 year ago
brianjohnhaas
commented
4 years ago Hi,
TransDecoder long orfs finds it, but as a longer 5' partial sequence that begins off the end of the contig.
Screenshot attached.
best,
~b
shamsbhuiyan
commented
4 years ago Hey, no screenshot was attached (at least that I can see). Would you be able to reupload it?
brianjohnhaas
commented
4 years ago 
shamsbhuiyan
commented
4 years ago Ah thanks. I'm a little confused by what 5' partial meant. I assumed it meant that there are inframe amino acids with a stop codon, but no start codon. Is my interpretation correct?
brianjohnhaas
commented
4 years ago yes, that's correct
shamsbhuiyan
commented
4 years ago But there is a start codon in frame within that ORF. So shouldn't it be a complete ORF (and also smaller?) The Transdecoder ORF is 268 AA but the ORF finder ORF is 204 AA.
On Tue, Feb 25, 2020 at 10:47 AM Brian Haas notifications@github.com wrote:
yes, that's correct
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brianjohnhaas
commented
4 years ago if the orf runs off the end of the contig, we start it at the end
On Tue, Feb 25, 2020 at 1:51 PM shamsbhuiyan notifications@github.com wrote:
But there is a start codon in frame within that ORF. So shouldn't it be a complete ORF (and also smaller?) The Transdecoder ORF is 268 AA but the ORF finder ORF is 204 AA.
On Tue, Feb 25, 2020 at 10:47 AM Brian Haas notifications@github.com wrote:
yes, that's correct
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shamsbhuiyan
commented
4 years ago But why?
On Tue, Feb 25, 2020 at 10:59 AM Brian Haas notifications@github.com wrote:
if the orf runs off the end of the contig, we start it at the end
On Tue, Feb 25, 2020 at 1:51 PM shamsbhuiyan notifications@github.com wrote:
But there is a start codon in frame within that ORF. So shouldn't it be a complete ORF (and also smaller?) The Transdecoder ORF is 268 AA but the ORF finder ORF is 204 AA.
On Tue, Feb 25, 2020 at 10:47 AM Brian Haas notifications@github.com wrote:
yes, that's correct
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brianjohnhaas
commented
4 years ago Occam's razor, I guess. It's unlikely for a long upstream region to be free of an intervening stop codon unless you have high GC content. Simplest explanation is that it's a 5' partial. If you had a longer sequence, you'd find the proper start, or a better one.
On Tue, Feb 25, 2020 at 2:08 PM shamsbhuiyan notifications@github.com wrote:
But why?
On Tue, Feb 25, 2020 at 10:59 AM Brian Haas notifications@github.com wrote:
if the orf runs off the end of the contig, we start it at the end
On Tue, Feb 25, 2020 at 1:51 PM shamsbhuiyan notifications@github.com wrote:
But there is a start codon in frame within that ORF. So shouldn't it be a complete ORF (and also smaller?) The Transdecoder ORF is 268 AA but the ORF finder ORF is 204 AA.
On Tue, Feb 25, 2020 at 10:47 AM Brian Haas notifications@github.com wrote:
yes, that's correct
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When I run the following sequence through transdecoder, it misses a complete ORF of 204 lengths (looking at the longest_orfs.pep file):
However if I run the exact same sequence through the NCBI's ORF finder, it finds the 204 amino acid sequence.: https://www.ncbi.nlm.nih.gov/orffinder/
The 204 amino acid sequence is the "correct" one, at least according to ensembl. Why does TransDecoder miss it? Thank you