Journal Article

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

Semin Lee and Tom L. Blundell

in Bioinformatics

Volume 25, issue 15, pages 1976-1977
Published in print August 2009 | ISSN: 1367-4803
Published online May 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp300

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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@cryst.bioc.cam.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  916 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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