ncbi-blast warning: Selenocysteine (U) at position ** replaced by X

Question

[dssouzadan]

Hi all, I just want to know what does this warning message means.

There's a way to suppress blast+ warings? The old blast has a flag -warnings as parameter, but the blast+ doesn't.

Answer 1

[Neilfws]

U is used as the one-letter amino acid code for selenocysteine, but it is not specified in the BLAST scoring matrices. So it is masked from the search by changing it to X.

Here's the Wikipedia page for selenocysteine. It's encoded by what would normally be a stop codon (UGA), but a special mechanism (translational recoding) exists for its insertion during translation. You can see that discoveries like this present problems for scoring matrices.

I don't know if the warnings can be suppressed, but they are no cause for concern.

[dssouzadan]

Thanks for your reply!