Additional file 5.

Unweighted total context bias in tranposons and non-repetitive sequence. Differences in total context bias between transposons and non-transposons might be due to variation in pattern frequencies rather than difference in the substitution process. To address this, we calculated an unweighted version of eq. 5 across all single-substitution patterns at each pattern size. To do this we simply replaced the term f(P) in eq. 5 with the term 1/N, where N is the total number of patterns. With this new measure, as with total context bias, we find that transposons have more bias than non-transposon sequence at all sizes.

Format: PDF Size: 46KB Download file

This file can be viewed with: Adobe Acrobat Reader

Nevarez et al. BMC Bioinformatics 2010 11:462   doi:10.1186/1471-2105-11-462