Hi everyone in newsgroup bionet.software,
It's very kind of Hamish, who sent me a very detail explain for single
letter amio-acid codes. I forward the mail to the newsgroup. Hope it
could help someone else.
On Mon, Jun 30, 2008 at 10:22 PM, Hamish McWilliam <hpm from ebi.ac.uk> wrote:
> Hi Linlin,
>> A brief description of the meanings of the single letter amino-acid codes
> can be found in the RESID FAQ (http://www.ebi.ac.uk/RESID/faq.html#q01).
>> In short 'J' is used for cases where the residue can be leucine ('L') or
> isoleucine ('I') and is a result of the use of mass-spec sequencing where
> the 'L' and 'I' cannot be distinguished. The 'B' (aspartic acid or
> asparagine) and 'Z' (glutamic acid or glutamine) codes have a similar
> function in chemical sequencing.
>> Note that 'O' (pyrrolysine) and 'U' (selenocysteine) are now appearing in
> the sequence databases (see http://beta.uniprot.org/news/2008/02/26/release> and
>http://www.ebi.ac.uk/embl/Documentation/Release_notes/relnotes89/relnotes.html#2.2).
> Currently not enough is known about the substitution rates of these residues
> for them to be included in the scoring matrices, so they are generally
> handled as unknown residues ('X').
>> I hope this helps,
>> Hamish
