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Fig. 5 | BMC Genomics

Fig. 5

From: Widespread of horizontal gene transfer in the human genome

Fig. 5

a The distributions of repeats of HGT regions. The proportions of different types of repeats, including SINEs, LINEs, LTRs, DNA repeats, simple repeats, low complexity, etc. in predicted HGT regions were shown. Each HGT sequences and franking regions were divided into five regions: window 1 (w1, 300 bps upstream of the sequences), window 2 (w2, the beginning 300 bps of the HGT regions), window 3 (w3, the middle regions of the HGT regions), windows 4 (w4, the ending 300 bps of the sequences), and windows 5 (w5, 300 bps downstream of the sequences). Besides, the distribution of repeat types for HGT regions and the whole human genome. b The Distribution of repeats within the HGT regions. We calculated the average proportions of different types of repeats in the five regions of our sequences and drew the average proportions curve of different types of repeats within the HGT regions and 1 kbps upstream and downstream of HGT regions. We can divide the X axis into six intervals: the interval from 0 to 300 bps means the 1 kbps upstream of HGT regions, the interval from 300 bps to 600 bps means the beginning 300 bps of HGT regions, the interval from 600 bps to 900 bps means the middle regions of HGT regions, the interval from 900 bps to 1200 bps means the ending 300 bps of HGT regions, the interval from 1200 bps to 1500 bps means the 300 bps downstream of HGT regions, the interval from 1500 bps to 1700 bps means the whole human genome. c and d GC contents and histone modification within the HGT regions. We calculated the GC content and drew GC content and histone modification curve for our sequences with a similar approach as the above section we did for repeats in Fig.5c, d. Our histone marks include H3K4Me1, H2A.Z, H3K4Me3, H3K9Ac, H3K27Ac, H3K27Me3, etc

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