TTG is translated to M

Open philipperuiz opened this issue 1 year ago • 1 comments

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 ?

Jul 17 '24 07:07 philipperuiz

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).

Jul 17 '24 09:07 althonos