Ulla: a program for calculating environment-specific amino acid substitution tables.
CONCLUSIONS
Amino acid residues are under various kinds of local environmental restraints, which influence substitution patterns. Ulla,(1) a program for calculating environment-specific substitution tables, reads protein sequence alignments and local environment annotations. The program produces a substitution table for every possible combination of environment features. Sparse data is handled using an entropy-based smoothing procedure to estimate robust substitution probabilities.


BACKGROUND
The Ruby source code is available under a Creative Commons Attribution-Noncommercial License along with additional documentation from http://www-cryst.bioc.cam.ac.uk/ulla.


BACKGROUND
Supplementary data are available at Bioinformatics online.
Lee
Semin
S
Department of Biochemistry, University of Cambridge, Old Addenbrooke's Site, Cambridge CB2 1GA, UK. semin@cryst.bioc.cam.ac.uk
Blundell
Tom L
TL
D019943:Amino Acid Substitution; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D012984:Software
D011506:Proteins