A good tool should leave "b" as is: it is ASX (the standard ambiguity
code for ASP or ASN). "j", "o" and "u" are a different matter :-)

http://www.uniprot.org/manual/non_std

"Selenocyteine [sic!] and pyrrolysine are represented in the sequence using the one-letter codes U for selenocysteine and O for pyrrolysine"

--Gerard

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                           Gerard J. Kleywegt

      http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
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   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
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   Little known gastromathematical curiosity: let "z" be the
   radius and "a" the thickness of a pizza. Then the volume
            of that pizza is equal to pi*z*z*a !
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