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Text: We used an in silico approach to identify useful restriction enzymes for subsequent DNA hybridizations to visualize HML-2 proviruses, and to generate a restriction fragment comparison from existing genome sequence **data** for reference during unblotting (see below). The HERV-K113 sequence (AY037928) was analyzed for restriction enzymes predicted to cut at least once within the provirus but not within the 5'LTR (NEBCutter2.0), for a total of 36 candidate enzymes. Simultaneously, we mined the 2009 human genome build (GRCh37/hg19) for proviruses with high percent identity to HML-2, again using the K113 nucleotide sequence as a reference. For the 32 proviruses identified from the search, we performed an in silico restriction analysis as follows. About 5 kb of sequence was extracted in both directions from the start of the 5'LTR. Each sequence was 'digested' in NEBCutterV2.0 for each of the 36 restriction sites with reference to a highly conserved sequence spanning bases 1017 to 1049 (5' CGTCGACTTC TTGTCCTCAATGACCACGC; HERVK-1017). For each enzyme analyzed, the estimated sizes for predicted HERV-K-containing junction fragments were plotted on a log scale for comparison. Based on restriction fragment estimates with reference to genome coverage and the observed fragment distribution, BsrI was selected for unblot analysis and coordinate in silico comparison to the published sequence.<|eot_id|><|start_header_id|>assistant<|end_header_id|>

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