Ulla: a program for calculating environment-specific amino acid substitution tables
نویسندگان
چکیده
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. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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عنوان ژورنال:
دوره 25 شماره
صفحات -
تاریخ انتشار 2009