Amino acid J?

[andreaswallberg]

Dear @ogotoh,

I have mapped protein sequences to a genome and observe in the alignment output (O1) that many codons that I expect to encode "S" or Serine are written as "J", which as far as I know may be an ambiguity code for "Xle" or "Leucine or Isoleucine".

Can you please explain what the J, or any such symbols, mean?

Thanks for a great tool!

[ogotoh]

Dear Andreas,

As explained in my paper “Homology-based gene structure prediction: simplified matching algorithm using a translated codon (tron) and improved accuracy by allowing for long gaps” (O. Gotoh, Bioinformatics, 16 (3) 190-202 (2000), ‘J’ implies the translated codon ‘AGY’, whereas ‘S’ implies the translate codon ‘TCN’. After translation ‘J’ is equivalent to ‘S’, so you may simply reread ‘J’ as ‘S’.

Osamu,

2023年6月15日(木) 19:24 Andreas Wallberg @.***>:

Dear @ogotoh https://github.com/ogotoh,

I have mapped protein sequences to a genome and observe in the alignment output (O1) that many codons that I expect to encode "S" or Serine are written as "J", which as far as I know may be an ambiguity code for "Xle" or "Leucine or Isoleucine".

Can you please explain what the J, or any such symbols, mean?

Thanks for a great tool!

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