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ERROR: inconsistency between the following pep and nuc seqs

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Bob Smith

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Nov 25, 2024, 4:45:27 AM11/25/24
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Hello, when I use pal2nal.pl to convert the aligned protein sequence to codon sequence based on cds sequence, it produces the following error, after checking, I found that it's because your script denotes the unknown amino acid site as *, whereas in NCBI's database, the unknown site is denoted by X, which leads to this error, how can I fix it?

error.png

Sandra AC

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Nov 26, 2024, 4:28:09 AM11/26/24
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Hi there,

Thanks for your message! Please note that PAL2NAL is not a PAML program, see Suyama et al. 2006. It seems to be hosted both as a server (see their website) and as a PERL script (there are various sources, e.g. this GitHub repository). Please address any questions regarding this script to the script developers :) 

All the best,
Sandy

Sishuo Wang

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Nov 28, 2024, 10:22:23 PM11/28/24
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Hi friend,

Seems that the translated seq according to your nucl seq and your input aa seq are not consistent, in which case pal2nal will call bl2seq from blast to identify the transalted seq, so you may want to install blast and its associated programs first. however, I think that a better practice might be to carefully check the AA seq and the condon seq, e.g. any codon shift, or if the codon table is correctly chosen (for example your organisms don't use the default codon table and you need to specify it)? If possible, we encourage you to upload the (misaligned) sequence to here.

best,
sishuo

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