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Comment
. 2008 Nov;4(11):e1000268.
doi: 10.1371/journal.pgen.1000268. Epub 2008 Nov 28.

A careful look at binding site reorganization in the even-skipped enhancers of Drosophila and sepsids

Emily E Hare  1 , Brant K Peterson, Michael B Eisen
Affiliations
Comment

A careful look at binding site reorganization in the even-skipped enhancers of Drosophila and sepsids

Emily E Hare et al. PLoS Genet. 2008 Nov.
No abstract available

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Figures

Figure 1
Figure 1. BLAST Similarity Maps of D. melanogaster even-skipped Stripe 2 Enhancer and Orthologous Enhancers from Drosophila and Sepsid Species.
We aligned the D. melanogaster even-skipped stripe 2 enhancer against the orthologous enhancers of D. pseudoobscura, D. virilis, T. putris, and Sepsis cynipsea (sequences as described in [1]) using NBCI BLAST bl2seq v2.2.17, with default parameters except –W (wordsize) = 9. For each species pair, high-scoring pairs (HSPs) above the default E-value cutoff of 10 were mapped by drawing a box connecting the start and end of the hit in the query and target sequence. Blue boxes represent forward strand hits, red boxes indicate reverse strand hits. The opacity of the color was scaled so that the highest scoring BLAST hits had maximal opacity of 1.0 and the lowest scoring hit had opacity of 0.1.
Figure 2
Figure 2. BLAST Similarity Maps of D. melanogaster even-skipped Stripe 2 Enhancer and Orthologous Enhancers.
We aligned the D. melanogaster even-skipped stripe 3/7, stripe 4/6 and MHE enhancers against the orthologous enhancers of T. putris (sequences as described in [1]) using NBCI BLAST bl2seq v2.2.17, with default parameters except –W (wordsize) = 9. For each species pair, HSPs above the default E-value cutoff of 10 were mapped by drawing a box connecting the start and end of the hit in the query and target sequence. Blue boxes represent forward strand hits, red boxes indicate reverse strand hits. The opacity of the color was scaled so that the highest scoring BLAST hits had maximal opacity of 1.0 and the lowest scoring hit had opacity of 0.1.
Figure 3
Figure 3. Predicted Binding Sites in the even-skipped Stripe 2 Enhancer of Drosophila and Sepsid Species.
Predicted binding sites for HB, BCD, GT, and KR in the even-skipped stripe 2 enhancers of four Drosophila and four sepsid species. Sites were predicted using PATSER using position-weight matrixes and cutoffs for each factor as described in . The height of the oval representing each predicted binding site, and the intensity of the color inside the oval, are proportional to the score of the hit.
Figure 4
Figure 4. Similarity Map of D. melanogaster even-skipped Stripe 2 Enhancer and Predicted Binding Sites in D. melanogaster and T. putris.
We compared all 20-bp windows in the D. melanogaster and T. putris even-skipped stripe 2 enhancers (sequences as described in [1]) and mapped regions with at least 14 identical base pairs. We have found that simple percent-identity plot gives a more reliable and robust measure of similarity that BLAST. We then predicted binding sites for HB, BCD, GT, and KR in both sequences using PATSER with position-weight matrixes and cutoffs for each factor as described in . The height of the oval representing each predicted binding site, and the intensity of the color inside the oval, are proportional to the score of the hit.
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References

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