compseq: is U an amino acid

[Gary Williams, Tel 01223 494522]

U codes for the amino acid selenocysteine.

See the IUPAC documentation for one-letter amino-acids:
http://www.chem.qmul.ac.uk/iupac/AminoAcid/A2021.html
and
http://www.chem.qmul.ac.uk/iubmb/newsletter/1999/item3.html

regards,
Gary

> "JAEN (Jacob Engelbrecht)" wrote:
> 
> I have been using compseq for protein sequences and wondered why 'U'
> is reported as an amino acid?
> I looked in the code (nucleus/embnmer.c) and found it was specifically
> accounted for, whereas 'X' which in many databases  as unknown is not
> specifically accounted for.
> 
> Would it not make sense to have options which made specific symbols
> part of the alphabet or left them out:
> -leaveout XU or -include BZXU
> 
> Jacob Engelbrecht, Phd
> Insulin Research
> Novo Nordisk
> 6A1.038 Novo Alle
> DK-2880 Bagsvaerd
> Denmark
> tel: +45 4442 4403
> mail: jaen at novonordisk.com

-- 
Gary Williams               Tel: +44 1223 494522  Fax: +44 1223 494512
mailto:G.Williams at hgmp.mrc.ac.uk            http://www.hgmp.mrc.ac.uk/
Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK