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Bioinformatics Advance Access originally published online on May 5, 2009
Bioinformatics 2009 25(15):1976-1977; doi:10.1093/bioinformatics/btp300
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Ulla: a program for calculating environment-specific amino acid substitution tables

Semin Lee * and Tom L. Blundell

Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Old Addenbrooke's Site, Cambridge CB2 1GA, UK

* To whom correspondence should be addressed.


  Abstract

Summary: 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.

Availability: 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.

Contact: semin{at}cryst.bioc.cam.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Anna Tramontano

Received on March 17, 2009; revised on April 18, 2009; accepted on April 28, 2009

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