It really depends on what you want to do with it but it would seems like a
good target for an Alphabet
- Mark
"Mark Southern" <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
04/05/2005 03:26 AM
To: <[email protected]>
cc: (bcc: Mark Schreiber/GP/Novartis)
Subject: [Biojava-l] Symbol / SymbolPropertyTable question
I thought I would ask the list for advice before I embarked on something.
I
have some physiochemical properties of amino acids that I would like to
access. (Milne Acid/Base Lambda/Rho) It includes values for modified amino
acids, side groups and N and C termini. See below.
I could of course do a very simple String -> value mapping. The question
is:
what would be the best way to implement this in biojava? I can imagine a
setup similar to ProteinTools which reads in per-symbol properties from
xml
and creates SymbolPropertyTable instances but in this example I have
modified amino acids and non-aa entities so I might need to create a new
Alphabet?
Cheers,
Mark.
ALANINE A
ARGININE R
ASPARTIC ACID D
ASP COOH D+
ASPARAGINE N
CYSTEIN C
CYSTINE C2
GLYCINE G
GLUTAMIC ACID E
GLU COOH E+
GLUTAMINE Q
HIS H
ISOLEUCINE I
LEUCINE L
LYSINE K
METHIONINE M
PHENYLALANINE F
PROLINE P
PRO cis Pc
SERINE S
THREONINE T
TRYPTOPHANE W
TYROSINE Y
VALINE V
N-Term NT
C-Term CT
-NHMe NMe
H3CCO- Ac
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