Codon-triplet context unveils unique features of the protein coding genome-8
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posted on 2011-12-31, 13:25 authored by Gabriela R Moura, José P Lousado, Miguel Pinheiro, Laura Carreto, Raquel M Silva, José L Oliveira, Manuel AS SantosCopyright information:
Taken from "Codon-triplet context unveils unique features of the protein coding genome"
http://www.biomedcentral.com/1471-2164/8/444
BMC Genomics 2007;8():444-444.
Published online 29 Nov 2007
PMCID:PMC2244636.
into a local database to eliminate false Open Reading Frames. Sequences were then processed by counting all codon-triplets, excluding the first and the last ones of each ORF, which have specific translation initiation and termination contexts. These data were transferred to a 3-dimensional 61 × 61 × 61 matrix and were saved as a Microsoft Access Database file. The processed data were then analyzed using Weka-3 data mining tools [19] and direct database queries. This methodology allowed us to handle very large data sets and identify differences in codon-triplet context between fungal species. These differences were finally subjected to statistical analyses.