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Furthermore, upstream genes (possibly also on the opposite strand) can also be taken as effective 5′-terminal positions of individual gene promoters hexamers comprising 2016 forward and reverse-complement hexamer pairs and 64 palindromic hexamers that are identical in forward- and reverse-complement orientation (see Note 4). 2 Motif Mapping 1. All 2080 unique hexamer motifs are to be mapped to all promoter sequences (Fig. 4a). 1, step 2). As mentioned above, 2016 motifs need to be mapped in both forward- and reverse-complement orientation, but are considered as hits of the same motif.

In classical phylogenetic footprinting, where different species are compared, the genes must correspond to orthologs. e. SNP-based motif discovery, vertically aligned genomic positions are almost guaranteed to result in correctly matched genes that can be taken as allelic variants of one another as those with low variability then need to be checked for novelty and the potentially novel motifs validated further. However, given the typical SNP-density, even in the case of hundreds of different individual genotype sequences are available, this naïve approach would result in nearly all sequence stretches to be identified as fully conserved.

29. If the synthetic promoters are expected to be highly responsive to environmental conditions, plants should be moved close to the CCD camera setup in advance of the experiment. We find that moving 4xRSRE:LUC plants 4 h prior to the start of imaging is sufficient. 30. 3, external shutter = fully auto, data type = counts. 31. The optimal exposure time must be empirically determined for each construct. The exposure should be at the shortest time that still allows for clear detection of the luciferase signal.

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Description des plantes rares cultivées à Malmaison et à Navarre by Aimé Bonpland

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