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Fig. 1 | Source Code for Biology and Medicine

Fig. 1

From: TRX-LOGOS - a graphical tool to demonstrate DNA information content dependent upon backbone dynamics in addition to base sequence

Fig. 1

TRX logo plots describing Shannon information content regarding base sequence and intrinsic DNA flexibility at single phosphate linkages in the DNA backbone at functionally confirmed transcription factor binding sites in the Saccharomyces cerevisiae genome. Note: lighter shaded bars indicate more flexible conformational states. Functionally confirmed consensus motifs from the Yeastract database were used to search and collect a very large sample of genomic TFBS. These sites were merged to match the 16 general JASPAR database classifications for TFBS. TRX logo plots for four of these merged categories are shown here. These are a Ig-fold Rel, b Copper Fist, c Homeobox and d MADS box. All 16 merged TRX-logos category plots are in Additional file 3. Categorizations used are also included in Additional file 3. 7 bp flanking regions were included

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Source Code for Biology and Medicine

ISSN: 1751-0473