CDS translation is broken with bacterial trans_table=11

[lfalquet]

Describe the bug
The translation into protein creates an issue when the translation table is set to "11" (bacterial code).

When the start codon is NOT a canonical "ATG" (e.g., GTG), the translation misses the quotes around the sequence.

FT /transl_table=11
FT /translation=GTGIRAGGCGIGCFPGKGEMEFRILGSVQIHDERFGVRIVPAGAKQ
FT RALLGALLVRAGQAVPAECLVEELWGGHPPVNAANALQAHVARLRRLLPAPGPGGPRHV
FT WLRTSPLGYTLSLGPAATDAQRFHRLVGQGRELAATAPGRAVEVLREGLALWRGPALQG
FT SGQGPICSAEAALLEESRLRALEVLYDVCLRADRCAEITGELEELVAVHPLRERFHEQL
FT MTALHRCGRRAEALSTYDRARRRLARDLGIGPGQVLSRRREAILRSCEPAADSADRAGA
FT GTAGQGGDELGVLREELVRLRGHVELLRRQQRELSEQVARLTAHHPCGP

It works correctly for the other CDS where the start codon is the canonical "ATG"

FT /transl_table=11
FT /translation="MEIKVLGALNAEFEGISVVPSAGKPRQILALLALYPGRVVPVPTL
FT MEEIWGTDLPQSSMTTLQTYILQLRRLLGTAMGPDVPGSAKDVLATRYGGYLLQIPAEA
FT VDAFTYERLVTEGRQAYEDGEDERAATVLRRALDLWDGPALVDVRVGPVLEIEAMRLEQ
FT SRLVARERRIDADLRLGRHVELIAELTDLIARHPQHEGLHSQAMVALYRSGRQAAALDV
FT YRRLRQRLIDELGVEPSPQLQRLHQAMLAVDPRLDIVAGPRRTSTFDLYAA"

Thanks for correcting this bug.

Best greetings,
Laurent

[lfalquet]

It also put "GTG" instead of "M", I have just noticed...

[Juke34]

Thank you for reporting this bug.

Have in mind that submitting translated CDS is not mandatory. EBI will make and add the translation.

[lfalquet]

Dear Jacques, OK thanks! That's exactly what I did (submission without CDS). Cheers Laurent Le 3 oct. 2024 à 20:43, Jacques Dainat ***@***.***> a écrit : This Message Is From an External Sender This message came from outside of the University of Fribourg. Please do not click links or open attachments unless you recognize the source of this email and know the content is safe. Thank you for reporting this bug. Have in mind that submitting translated CDS is not mandatory. EBI will make and add the translation. — Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https://github.com/NBISweden/EMBLmyGFF3/issues/86*issuecomment-2392087530__;Iw!!Dc8iu7o!2x1JIntkWUKnyVPmmUi4gsgk-TVkJ91bGJbjnuDs5eNZ1-T_yLmRtpY_fC4yo8Wo6ePiOQ3Iqgrtk-1Afhiq9BOR4QQ4Oao$>, or unsubscribe<https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/ABVKBPEYPXGP5EDGQZZ4NU3ZZWF5ZAVCNFSM6AAAAABPHCWPS6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGOJSGA4DONJTGA__;!!Dc8iu7o!2x1JIntkWUKnyVPmmUi4gsgk-TVkJ91bGJbjnuDs5eNZ1-T_yLmRtpY_fC4yo8Wo6ePiOQ3Iqgrtk-1Afhiq9BORYdUzMz4$>. You are receiving this because you authored the thread.

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----------------------------------------- Dr. Laurent Falquet (MA/MER) University of Fribourg Department of Biology Chemin du Musée 10 CH-1700 Fribourg, Switzerland Tel: +41 26 300 8991 Email: ***@***.*** Building: PER01 office O.366b SIB | Swiss Institute of Bioinformatics