How to resolve the error of protein lacking a stop codon when using GenomeThreader for homology prediction?
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12 weeks ago
peanut • 0

Dear all,the error message and running process are as follows. Thank you for your answers.


makeblastdb -in pudorinus.fa -parse_seqids -dbtype nucl -out index/pu&

nohup tblastn -query all.pep.fa -out pu.blast -db index/pu -outfmt 6 -evalue 1e-10 -num_threads 8 -qcov_hsp_perc 50.0 -num_alignments 5 &

awk '{print $1}' pu.blast >pu.list

sort pu.list| unique >pi.ho.list

seqkit seq all.pep.fa -w 0 > all.fa

vi sh.sh cat pi.ho.list | while read line do grep "$line"-A 1 all.fa >$line.1 done cat .1 > pudorinus.homo.fa rm -rf .1


gth -genomic pudorinus.fa -protein pudorinus.homo.fa -intermediate -gff3out > pudorinus.gff

warning: protein sequence 'Quercus_variabilis00000058.1'(#0 in file Q_gilva.homo.fa) does not end with a stop amino acid ('*').If it is not a protein fragment you should add a stop amino acid to improve the prediction. For example with gt seqtransform addstopaminos (see http://genometools.org for details).

genome threader • 857 views
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It seems like the solution if offered in the warning. Ensure that the protein is not a fragment, and if so, then add a stop codon. It even provides a tool to do it. If the protein is a fragment, remove it.

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Thank you for your answer,but after verifying the protein file, it seems there is no problem. Even if there are missing codons, the program should still be able to run. We suspect that GenomeThreader may have parameters to ignore this issue, so we are asking if anyone has had the same problem. Anyway,Thank you for your response.

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Ah, there is nothing in your post to suggest you are looking for a specific parameter to ignore a specific warning. I would suggest you edit your post to include what you are explicitly looking for. Potentially even including a few sequences to as we also cannot verify whether they are indeed correct.

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"Okay.Thank you very much."

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