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TTG is translated to M #58

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philipperuiz opened this issue Jul 17, 2024 · 1 comment
Open

TTG is translated to M #58

philipperuiz opened this issue Jul 17, 2024 · 1 comment
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@philipperuiz
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Hi, as Prodigal v2.6.3, we observe with pyrodigal a difference in translation result for some start codon (TTG).

nuc sequence (Lactobacillus)
TTGGGCATACCGGCTGAATACGTCTTATTCGACAGCTGTTTCTCTTCACCTAAAATGTTCTGGCAGCTGAAACAATTAGGGTTAGACAGCGTAGGCATGCTTAAGCGGACCAAGAAAGCTTATTATCGTTACCGTGGCCGACTTTATGATGTCAAAGGCCTGTACGAGCGCTTAGCTGCTTCCAAAATGCGTCAAAAAGAAGACTATCCCTATAGCAGCGTGGTCGAACCTGAATATCAGGGACATGTTTTCCAAATTAGATTAGTCTATGTCACTAAGCGCGGCGGTAAAGGAAAATATTTGGTACTGGTAACCACGCAATACAAGCTGCGATCAAAGTATTGCACGTCTTCTATGACAAGTGGAACAGAGCTTATAATCATGTCATAA

Prodigal / pyrodigal output
MGIPAEYVLFDSCFSSPKMFWQLKQLGLDSVGMLKRTKKAYYRYRGRLYDVKGLYERLAASKMRQKEDYPYSSVVEPEYQGHVFQIRLVYVTKRGGKGKYLVLVTTQYKLRSKYCTSSMTSGTELIIMS*

Expected sequence (Expasy 5'3' Frame 1)
LGIPAEYVLFDSCFSSPKMFWQLKQLGLDSVGMLKRTKKAYYRYRGRLYDVKGLYERLAASKMRQKEDYPYSSVVEPEYQGHVFQIRLVYVTKRGGGKYLVLVTTQYKLRSKYCTSSMTSGTELIIMS*

Maybe it is due to the use of wrong genetic code in this case ?
@philipperuiz philipperuiz changed the title GTG is translated to M TTG is translated to M Jul 17, 2024
@althonos
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althonos commented Jul 17, 2024 •
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This looks like it has been fixed in later versions, v3.4.1 doesn't seem to have that problem.
(at least when I'm testing with just the given sequence).

@althonos althonos added the bug Something isn't working label Jul 17, 2024
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@althonos @philipperuiz