You can see that the gene for PBP2_ECOLI has a 100% match inside the genome of O104:H4. Now that we have this list, we can answer some interesting questions, such as “How many of the known drug resistance genes are inside O104:H4?” I find it fascinating that this question is answered with a shell script: cat uniprot_search_m9 | awk '{if ($3 > 99) { print;}}' | cut -f2 |grep -v ^# | cut -f1 -d"_" | cut -f3 -d"|" | sort | uniq | wc -l The above script tells us that 1138 genes are a 100% match against the database of 1378 genes. If you loosen the criteria up to a 99% match, allowing for 1 or 2 mutations per gene — possibly a result of sequencing errors or just evolution — the list expands to 1224 out of 1378.

grepping the genome of e.coli for cure clues

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