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Escherichia coli strain K-12, substrain DH10B 4,126 proteins, 3,797 families Escherichia coli strain K-12, substrain W3110 4,226 proteins, 3,965 families Escherichia coli strain K-12, substrain MG1655 4,150 proteins, 3,912 families 4.3 % 167 / 3,912 95.3 % 3,843 / 4,034 91.5 % 3,685 / 4,027 4.3 % 170 / 3,965 93.1 % 3,742 / 4,020 Escherichia coli strain K-12, substrain MG1655 4,150 proteins, 3,912 families 6.4 % 242 / 3,797 Escherichia coli strain K-12, substrain W3110 4,226 proteins, 3,965 families Comparative Genomics Escherichia coli strain K-12, substrain DH10B 4,126 proteins, 3,797 families Figure 2.9: Construction of the BLASTmatrix diagram. Proteome similarity between three E. coli genomes. Lower part of the diagram corresponds to intra-proteome similarity. lari jejuni concisus curvus fetus hominis 2.3 % 34 / 1,494 57.2 % 1,123 / 1,965 Campylobacter fetus subsp. fetus 82-40 1,719 proteins, 1,665 families Campylobacter hominis ATCC BAA-381 1,687 proteins, 1,623 families Campylobacter jejuni RM1221 1,838 proteins, 1,780 families Campylobacter jejuni subsp. doylei 269.97 1,731 proteins, 1,650 families Campylobacter jejuni subsp. jejuni 81-176 1,758 proteins, 1,702 families Campylobacter jejuni subsp. jejuni 81116 1,626 proteins, 1,585 families Campylobacter jejuni subsp. jejuni NCTC 11168 1,624 proteins, 1,581 families Campylobacter lari RM2100 1,546 proteins, 1,494 families 56.7 % 1,123 / 1,979 1.7 % 27 / 1,581 55.2 % 1,145 / 2,073 84.7 % 1,448 / 1,709 Campylobacter concisus 13826 2,080 proteins, 1,972 families Campylobacter curvus 525.92 1,931 proteins, 1,885 families 49.4 % 1,062 / 2,150 83.5 % 1,481 / 1,773 1.5 % 24 / 1,585 53.0 % 1,143 / 2,158 67.3 % 1,316 / 1,955 82.9 % 1,474 / 1,778 22.8 % 596 / 2,619 76.9 % 1,466 / 1,906 64.4 % 1,289 / 2,003 2.3 % 39 / 1,702 30.0 % 742 / 2,476 22.9 % 614 / 2,676 74.6 % 1,441 / 1,931 62.2 % 1,304 / 2,096 24.7 % 682 / 2,756 30.6 % 774 / 2,526 23.1 % 617 / 2,675 71.4 % 1,451 / 2,032 4.0 % 66 / 1,650 24.5 % 704 / 2,875 24.8 % 698 / 2,820 30.3 % 770 / 2,538 22.5 % 628 / 2,795 63.5 % 1,345 / 2,118 Campylobacter lari RM2100 24.4 % 718 / 2,948 25.1 % 706 / 2,816 28.7 % 767 / 2,669 21.2 % 595 / 2,802 2.3 % 41 / 1,780 1,546 proteins, 1,494 families Campylobacter jejuni subsp. jejuni NCTC 11168 1,624 proteins, 1,581 families 24.3 % 717 / 2,950 23.7 % 699 / 2,950 27.5 % 736 / 2,676 21.4 % 618 / 2,886 Campylobacter jejuni subsp. jejuni 81116 1,626 proteins, 1,585 families 23.6 % 723 / 3,070 22.5 % 668 / 2,964 27.9 % 767 / 2,750 2.0 % 33 / 1,623 22.7 % 698 / 3,076 23.0 % 698 / 3,036 30.4 % 782 / 2,576 22.5 % 713 / 3,175 26.1 % 741 / 2,838 1.5 % 25 / 1,665 lari Campylobacter jejuni subsp. jejuni 81-176 1,758 proteins, 1,702 families Campylobacter jejuni subsp. doylei 269.97 1,731 proteins, 1,650 families Campylobacter jejuni RM1221 25.8 % 765 / 2,961 34.7 % 929 / 2,678 1,838 proteins, 1,780 families 32.4 % 916 / 2,828 1.8 % 34 / 1,885 50.3 % 1,317 / 2,616 jejuni Campylobacter hominis ATCC BAA-381 1,687 proteins, 1,623 families Campylobacter fetus subsp. fetus 82-40 1,719 proteins, 1,665 families Campylobacter curvus 525.92 3.5 % 69 / 1,972 1.5 % Homology between proteomes 1,931 proteins, 1,885 families Campylobacter concisus 13826 2,080 proteins, 1,972 families hominis fetus curvus concisus Homology within proteomes Figure 2.10: Proteome similarity between ten Campylobacter species. Color encoding corresponds to percentage of shared protein families. 21.2 % 84.7 % 4.0 % 17
Genome Comparisons A.salmonicida LFI1238 V.species Ex25 V.campbellii AND4 V.harveyi BAA1116 V.shilonii AK1 P.profundum SS9 27.2 % 1,946 / 7,165 27.1 % 31.2 % 1,964 / 7,245 2,143 / 6,862 27.5 % 31.1 % 32.5 % 1,971 / 7,179 2,163 / 6,948 2,385 / 7,336 26.3 % 31.5 % 32.6 % 35.8 % 1,893 / 7,208 2,169 / 6,884 2,405 / 7,380 2,018 / 5,637 28.0 % 30.4 % 33.1 % 35.9 % 38.7 % 1,962 / 7,016 2,098 / 6,893 2,415 / 7,299 2,049 / 5,713 2,143 / 5,536 28.7 % 32.3 % 31.7 % 36.4 % 38.3 % 32.1 % 1,944 / 6,766 2,164 / 6,706 2,323 / 7,337 2,055 / 5,647 2,156 / 5,631 1,846 / 5,747 28.2 % 33.0 % 33.6 % 34.7 % 38.8 % 32.1 % 34.0 % 1,960 / 6,957 2,137 / 6,467 2,410 / 7,181 1,968 / 5,677 2,162 / 5,566 1,873 / 5,828 1,963 / 5,771 27.6 % 32.4 % 34.3 % 37.3 % 37.9 % 32.5 % 33.7 % 35.0 % 1,965 / 7,122 2,155 / 6,649 2,377 / 6,932 2,045 / 5,477 2,110 / 5,560 1,873 / 5,769 1,977 / 5,865 1,949 / 5,561 27.7 % 31.8 % 33.8 % 38.7 % 40.3 % 30.6 % 34.2 % 34.8 % 40.3 % 1,965 / 7,093 2,169 / 6,817 2,403 / 7,116 2,021 / 5,225 2,167 / 5,378 1,777 / 5,804 1,983 / 5,797 1,967 / 5,647 2,326 / 5,771 27.8 % 32.1 % 33.3 % 37.4 % 41.6 % 33.3 % 32.5 % 35.3 % 39.8 % 38.4 % 1,967 / 7,064 2,173 / 6,778 2,418 / 7,252 2,032 / 5,428 2,140 / 5,139 1,863 / 5,593 1,896 / 5,827 1,972 / 5,581 2,339 / 5,873 2,291 / 5,971 25.7 % 32.2 % 33.5 % 36.7 % 40.6 % 34.4 % 35.3 % 33.6 % 40.4 % 38.0 % 41.7 % 1,850 / 7,198 2,173 / 6,752 2,420 / 7,225 2,048 / 5,585 2,159 / 5,323 1,846 / 5,360 1,981 / 5,619 1,884 / 5,612 2,345 / 5,808 2,307 / 6,067 2,552 / 6,116 25.6 % 30.3 % 33.6 % 37.0 % 39.5 % 33.4 % 36.6 % 36.3 % 38.6 % 38.5 % 41.2 % 44.3 % 1,841 / 7,194 2,079 / 6,856 2,420 / 7,193 2,051 / 5,545 2,169 / 5,493 1,852 / 5,547 1,964 / 5,371 1,965 / 5,413 2,251 / 5,839 2,311 / 6,004 2,564 / 6,224 2,515 / 5,683 28.1 % 29.7 % 31.0 % 37.2 % 39.7 % 32.7 % 35.5 % 37.7 % 41.7 % 37.0 % 41.9 % 43.7 % 42.2 % 1,904 / 6,782 2,044 / 6,887 2,282 / 7,362 2,052 / 5,516 2,168 / 5,459 1,868 / 5,705 1,974 / 5,563 1,947 / 5,165 2,346 / 5,626 2,227 / 6,026 2,575 / 6,151 2,527 / 5,781 2,215 / 5,254 26.9 % 32.4 % 30.8 % 34.4 % 40.0 % 33.0 % 34.6 % 36.6 % 42.9 % 39.7 % 40.0 % 44.5 % 41.6 % 40.0 % 1,851 / 6,869 2,098 / 6,481 2,270 / 7,379 1,944 / 5,645 2,171 / 5,428 1,872 / 5,667 1,982 / 5,732 1,961 / 5,354 2,314 / 5,388 2,312 / 5,825 2,473 / 6,185 2,539 / 5,707 2,225 / 5,354 2,421 / 6,055 28.2 % 31.2 % 33.3 % 34.8 % 38.2 % 33.2 % 34.8 % 35.7 % 41.9 % 40.6 % 42.9 % 42.8 % 42.3 % 39.6 % 70.3 % 1,949 / 6,915 2,045 / 6,565 2,327 / 6,984 1,952 / 5,606 2,104 / 5,504 1,872 / 5,641 1,984 / 5,694 1,969 / 5,522 2,334 / 5,571 2,270 / 5,592 2,564 / 5,977 2,449 / 5,718 2,236 / 5,283 2,438 / 6,154 2,933 / 4,174 27.9 % 32.6 % 32.1 % 38.1 % 37.3 % 30.2 % 35.0 % 35.9 % 40.9 % 39.9 % 44.1 % 45.9 % 41.3 % 40.0 % 69.2 % 73.6 % 1,942 / 6,969 2,153 / 6,600 2,268 / 7,062 1,994 / 5,228 2,064 / 5,537 1,747 / 5,786 1,985 / 5,667 1,971 / 5,485 2,343 / 5,733 2,299 / 5,768 2,533 / 5,743 2,535 / 5,526 2,181 / 5,277 2,440 / 6,094 2,953 / 4,267 3,045 / 4,135 27.9 % 31.8 % 34.2 % 36.4 % 41.6 % 30.0 % 31.9 % 36.1 % 41.2 % 38.9 % 43.3 % 47.1 % 43.8 % 38.4 % 69.7 % 74.9 % 71.6 % 1,941 / 6,954 2,123 / 6,682 2,394 / 7,002 1,935 / 5,317 2,134 / 5,135 1,736 / 5,791 1,857 / 5,817 1,971 / 5,458 2,346 / 5,697 2,309 / 5,932 2,559 / 5,916 2,503 / 5,310 2,234 / 5,101 2,348 / 6,120 2,944 / 4,221 3,101 / 4,142 3,010 / 4,205 27.9 % 32.0 % 33.4 % 37.7 % 39.1 % 33.6 % 32.1 % 32.8 % 41.4 % 39.3 % 42.3 % 46.4 % 45.9 % 41.4 % 66.3 % 75.5 % 72.6 % 75.9 % 1,909 / 6,851 2,130 / 6,656 2,359 / 7,060 2,026 / 5,367 2,048 / 5,244 1,805 / 5,377 1,861 / 5,795 1,843 / 5,611 2,346 / 5,670 2,314 / 5,892 2,572 / 6,075 2,534 / 5,464 2,223 / 4,842 2,445 / 5,905 2,833 / 4,271 3,089 / 4,092 3,068 / 4,226 3,094 / 4,077 29.6 % 32.0 % 33.4 % 37.3 % 40.4 % 31.9 % 35.6 % 33.1 % 38.0 % 39.4 % 42.7 % 45.2 % 44.3 % 42.4 % 73.2 % 69.8 % 73.5 % 77.2 % 68.7 % 2,295 / 7,753 2,097 / 6,549 2,375 / 7,115 2,022 / 5,418 2,139 / 5,293 1,743 / 5,469 1,922 / 5,398 1,848 / 5,585 2,213 / 5,823 2,314 / 5,868 2,578 / 6,032 2,546 / 5,633 2,232 / 5,038 2,408 / 5,683 2,952 / 4,034 2,942 / 4,217 3,065 / 4,172 3,155 / 4,088 2,874 / 4,181 27.9 % 35.2 % 33.0 % 37.3 % 39.4 % 33.5 % 34.2 % 36.7 % 38.0 % 36.9 % 42.9 % 45.5 % 43.0 % 41.8 % 73.5 % 76.0 % 68.5 % 78.0 % 67.2 % 70.4 % 1,972 / 7,061 2,581 / 7,333 2,325 / 7,056 2,019 / 5,407 2,118 / 5,370 1,845 / 5,501 1,872 / 5,473 1,906 / 5,192 2,209 / 5,811 2,208 / 5,989 2,579 / 6,005 2,548 / 5,599 2,240 / 5,212 2,434 / 5,818 2,863 / 3,897 3,059 / 4,025 2,914 / 4,256 3,149 / 4,038 2,880 / 4,288 2,922 / 4,153 29.4 % 34.3 % 46.4 % 37.8 % 40.3 % 32.9 % 35.7 % 34.9 % 41.8 % 36.4 % 39.4 % 45.8 % 43.4 % 40.8 % 76.4 % 75.2 % 74.1 % 71.5 % 69.7 % 70.3 % 64.7 % 2,212 / 7,534 2,276 / 6,634 3,371 / 7,266 2,001 / 5,288 2,145 / 5,320 1,824 / 5,545 1,970 / 5,513 1,843 / 5,282 2,264 / 5,418 2,186 / 6,003 2,432 / 6,172 2,552 / 5,568 2,242 / 5,171 2,445 / 5,993 2,970 / 3,887 2,954 / 3,928 3,024 / 4,083 2,986 / 4,175 2,916 / 4,183 2,965 / 4,217 2,888 / 4,463 27.8 % 34.4 % 34.9 % 47.0 % 39.8 % 33.0 % 34.9 % 36.8 % 39.9 % 39.9 % 39.1 % 42.2 % 43.6 % 41.1 % 73.1 % 80.4 % 73.0 % 79.5 % 69.0 % 72.2 % 64.9 % 76.9 % 2,222 / 7,979 2,472 / 7,184 2,496 / 7,160 2,741 / 5,827 2,086 / 5,245 1,831 / 5,549 1,952 / 5,586 1,951 / 5,307 2,202 / 5,514 2,238 / 5,609 2,413 / 6,176 2,409 / 5,711 2,244 / 5,143 2,450 / 5,957 2,977 / 4,072 3,080 / 3,831 2,908 / 3,986 3,125 / 3,932 2,860 / 4,145 2,986 / 4,136 2,940 / 4,533 3,165 / 4,117 28.1 % 33.0 % 38.7 % 37.8 % 64.9 % 33.1 % 35.2 % 36.1 % 42.0 % 38.0 % 43.0 % 41.4 % 41.1 % 41.3 % 73.4 % 77.3 % 78.5 % 77.9 % 71.8 % 68.5 % 67.6 % 76.7 % 83.4 % 2,155 / 7,667 2,516 / 7,615 2,880 / 7,439 2,081 / 5,503 3,384 / 5,214 1,804 / 5,448 1,954 / 5,558 1,940 / 5,373 2,320 / 5,530 2,171 / 5,707 2,483 / 5,781 2,372 / 5,735 2,153 / 5,242 2,449 / 5,936 2,971 / 4,050 3,098 / 4,009 3,061 / 3,901 3,002 / 3,856 2,896 / 4,036 2,869 / 4,191 2,983 / 4,413 3,195 / 4,167 3,315 / 3,973 29.5 % 36.5 % 37.0 % 39.9 % 45.0 % 31.9 % 35.3 % 36.2 % 41.1 % 40.1 % 40.1 % 46.3 % 41.2 % 37.9 % 73.8 % 77.1 % 75.8 % 83.0 % 71.5 % 73.7 % 65.1 % 81.6 % 81.3 % 82.4 % 2,198 / 7,456 2,593 / 7,105 2,900 / 7,832 2,372 / 5,942 2,357 / 5,232 2,074 / 6,494 1,926 / 5,455 1,940 / 5,352 2,303 / 5,603 2,293 / 5,719 2,373 / 5,919 2,464 / 5,326 2,152 / 5,228 2,313 / 6,099 2,975 / 4,030 3,088 / 4,007 3,073 / 4,056 3,135 / 3,777 2,801 / 3,915 2,947 / 4,001 2,880 / 4,423 3,264 / 4,000 3,320 / 4,085 3,302 / 4,009 30.3 % 36.7 % 34.6 % 37.5 % 46.1 % 32.3 % 35.5 % 36.3 % 41.6 % 39.2 % 43.5 % 43.5 % 46.0 % 38.2 % 65.6 % 78.0 % 75.1 % 79.4 % 72.2 % 81.0 % 67.3 % 77.5 % 81.9 % 80.8 % 83.2 % 2,110 / 6,968 2,562 / 6,982 2,682 / 7,762 2,396 / 6,387 2,626 / 5,697 1,842 / 5,705 2,270 / 6,400 1,906 / 5,250 2,314 / 5,569 2,272 / 5,796 2,550 / 5,859 2,367 / 5,437 2,220 / 4,821 2,320 / 6,080 2,791 / 4,256 3,097 / 3,971 3,061 / 4,077 3,144 / 3,961 2,861 / 3,960 2,989 / 3,688 2,909 / 4,320 3,153 / 4,066 3,311 / 4,041 3,319 / 4,106 3,325 / 3,995 29.7 % 30.4 % 36.7 % 36.9 % 43.2 % 32.6 % 34.5 % 35.9 % 41.5 % 39.8 % 42.2 % 45.9 % 42.7 % 42.3 % 65.2 % 71.3 % 76.3 % 79.3 % 69.0 % 74.9 % 67.8 % 78.4 % 76.3 % 81.6 % 80.7 % 85.8 % 2,127 / 7,169 2,085 / 6,866 2,759 / 7,516 2,259 / 6,124 2,655 / 6,143 2,040 / 6,250 1,965 / 5,696 2,233 / 6,219 2,272 / 5,479 2,292 / 5,756 2,506 / 5,941 2,501 / 5,451 2,113 / 4,953 2,399 / 5,675 2,768 / 4,246 2,953 / 4,142 3,076 / 4,029 3,138 / 3,958 2,868 / 4,158 2,944 / 3,932 2,836 / 4,184 3,157 / 4,029 3,142 / 4,120 3,311 / 4,057 3,321 / 4,117 3,291 / 3,837 28.3 % 29.4 % 29.6 % 38.6 % 40.2 % 30.5 % 35.3 % 36.2 % 43.9 % 39.2 % 42.9 % 46.1 % 44.3 % 39.7 % 71.6 % 70.2 % 69.2 % 80.3 % 69.1 % 73.3 % 68.1 % 74.3 % 83.7 % 75.3 % 81.4 % 82.5 % 79.6 % 1,980 / 6,989 2,083 / 7,082 2,214 / 7,478 2,289 / 5,931 2,413 / 5,999 2,050 / 6,715 2,191 / 6,211 1,976 / 5,464 2,762 / 6,293 2,230 / 5,684 2,536 / 5,906 2,513 / 5,455 2,213 / 5,001 2,303 / 5,796 2,802 / 3,915 2,930 / 4,172 2,925 / 4,226 3,147 / 3,918 2,864 / 4,145 2,983 / 4,071 2,876 / 4,226 2,987 / 4,018 3,275 / 3,915 3,136 / 4,162 3,309 / 4,067 3,278 / 3,971 3,139 / 3,944 28.0 % 26.7 % 29.3 % 33.6 % 42.3 % 33.1 % 33.1 % 36.3 % 45.4 % 41.4 % 42.3 % 45.7 % 43.5 % 42.9 % 68.6 % 77.2 % 64.3 % 73.1 % 70.0 % 73.6 % 66.4 % 78.6 % 86.6 % 82.6 % 76.0 % 83.4 % 78.1 % 92.9 % 2,022 / 7,222 1,916 / 7,168 2,244 / 7,665 1,915 / 5,695 2,451 / 5,795 2,074 / 6,269 2,209 / 6,672 2,179 / 6,005 2,507 / 5,523 2,698 / 6,523 2,475 / 5,845 2,506 / 5,480 2,200 / 5,058 2,463 / 5,745 2,743 / 4,001 2,983 / 3,866 2,805 / 4,365 3,000 / 4,103 2,873 / 4,102 2,979 / 4,045 2,917 / 4,393 3,113 / 3,962 3,253 / 3,757 3,267 / 3,954 3,147 / 4,141 3,267 / 3,919 3,147 / 4,032 3,489 / 3,754 25.5 % 34.5 % 28.3 % 32.5 % 34.5 % 34.9 % 35.7 % 34.2 % 43.7 % 43.7 % 46.4 % 45.1 % 44.9 % 40.8 % 77.1 % 71.8 % 71.6 % 69.5 % 68.3 % 74.3 % 66.3 % 75.5 % 91.2 % 85.6 % 82.9 % 79.4 % 80.2 % 89.7 % 77.1 % 1,872 / 7,339 2,335 / 6,762 2,095 / 7,406 1,919 / 5,903 1,963 / 5,692 2,114 / 6,065 2,219 / 6,213 2,205 / 6,448 2,670 / 6,112 2,492 / 5,705 3,042 / 6,550 2,444 / 5,415 2,242 / 4,998 2,400 / 5,876 2,975 / 3,861 2,855 / 3,974 2,868 / 4,006 2,908 / 4,185 2,820 / 4,126 2,982 / 4,014 2,908 / 4,386 3,125 / 4,141 3,355 / 3,679 3,244 / 3,790 3,277 / 3,954 3,143 / 3,956 3,169 / 3,953 3,485 / 3,884 3,186 / 4,134 26.1 % 30.9 % 43.4 % 30.3 % 33.9 % 55.5 % 38.1 % 36.6 % 40.8 % 41.9 % 43.2 % 48.9 % 43.5 % 42.4 % 73.0 % 82.5 % 67.9 % 76.7 % 68.0 % 68.5 % 67.0 % 74.6 % 91.7 % 90.1 % 83.2 % 87.0 % 75.1 % 81.1 % 74.9 % 80.4 % 2,254 / 8,624 2,144 / 6,948 2,981 / 6,875 1,795 / 5,923 1,991 / 5,874 2,683 / 4,838 2,277 / 5,979 2,201 / 6,016 2,680 / 6,565 2,637 / 6,301 2,597 / 6,013 2,994 / 6,128 2,155 / 4,958 2,451 / 5,781 2,911 / 3,989 3,117 / 3,780 2,780 / 4,092 2,961 / 3,861 2,806 / 4,126 2,844 / 4,150 2,915 / 4,348 3,103 / 4,160 3,455 / 3,766 3,346 / 3,715 3,208 / 3,855 3,272 / 3,762 3,024 / 4,028 3,280 / 4,046 3,187 / 4,253 3,303 / 4,109 25.9 % 30.1 % 45.0 % 46.2 % 30.5 % 52.4 % 75.0 % 38.7 % 72.3 % 39.7 % 67.5 % 47.2 % 43.5 % 40.9 % 74.7 % 78.0 % 78.6 % 71.8 % 73.1 % 70.6 % 64.7 % 75.4 % 96.0 % 90.4 % 91.4 % 83.0 % 80.7 % 77.3 % 80.2 % 88.8 % 88.1 % 2,170 / 8,370 2,581 / 8,574 3,018 / 6,702 2,452 / 5,307 1,813 / 5,939 2,666 / 5,085 3,261 / 4,346 2,246 / 5,808 3,688 / 5,101 2,672 / 6,728 3,741 / 5,540 2,608 / 5,524 2,547 / 5,858 2,360 / 5,769 2,922 / 3,914 3,045 / 3,906 3,059 / 3,894 2,849 / 3,968 2,818 / 3,854 2,886 / 4,087 2,847 / 4,403 3,111 / 4,124 3,531 / 3,678 3,439 / 3,805 3,373 / 3,689 3,126 / 3,768 3,108 / 3,853 3,164 / 4,093 3,271 / 4,079 3,489 / 3,927 3,495 / 3,966 5.0 % 243 / 4,897 3.9 % 200 / 5,078 3.9 % 201 / 5,117 V.parahaemolyticus 2210633 V.parahaemolyticus 16 V.vulnificus CMCP6 V.vulnificus YJ016 V.species MED222 V.splendidus LGP32 V.fischeri ES114 V.fischeri MJ11 2.3 % 88 / 3,822 2.7 % 103 / 3,886 3.3 % 111 / 3,378 2.9 % 112 / 3,894 2.6 % 96 / 3,691 2.8 % 118 / 4,277 2.3 % 103 / 4,463 3.1 % 150 / 4,773 V.cholerae MO10 V.cholerae BX330286 V.cholerae RC9 V.cholerae MJ1236 V.cholerae B33VCE V.cholerae 2740-80 V.cholerae AM-19226 V.cholerae MZO-2 V.cholerae 12129 V.cholerae TM11079-80 V.cholerae TMA21 V.cholerae VL426 V.cholerae 1587 2.8 % 121 / 4,337 2.1 % 79 / 3,683 V.cholerae N16961 V.cholerae 0395 TEDA V.cholerae 0395 TIGR V.cholerae V52 V.cholerae M66-2 3.2 % 147 / 4,662 1.9 % 62 / 3,316 2.9 % 99 / 3,427 P.profundum SS9 2.4 % 83 / 3,442 V.shilonii AK1 V.harveyi BAA1116 2.1 % 72 / 3,454 V.campbellii AND4 V.species Ex25 2.2 % 73 / 3,311 A.salmonicida LFI1238 V.fischeri MJ11 2.5 % 84 / 3,305 V.fischeri ES114 V.splendidus LGP32 2.8 % 99 / 3,586 V.species MED222 V.vulnificus YJ016 3.5 % 125 / 3,567 V.vulnificus CMCP6 V.parahaemolyticus 16 2.6 % 92 / 3,593 V.parahaemolyticus 2210633 V.cholerae VL426 3.0 % 109 / 3,575 V.cholerae TMA21 V.cholerae TM11079-80 2.8 % 102 / 3,619 V.cholerae 12129 V.cholerae MZO-2 2.9 % 100 / 3,429 V.cholerae AM-19226 V.cholerae 1587 1.8 % 59 / 3,353 30.0 % V.cholerae 2740-80 V.cholerae B33VCE 2.8 % 99 / 3,560 0.0 % Homology between proteomes Homology within proteomes V.cholerae MJ1236 V.cholerae RC9 3.3 % 120 / 3,599 V.cholerae BX330286 V.cholerae MO10 4.3 % 157 / 3,665 V.cholerae M66-2 V.cholerae V52 4.2 % 155 / 3,729 V.cholerae 0395 TIGR V.cholerae 0395 TEDA 3.0 % 110 / 3,665 90.0 % 6.0 % V.cholerae N16961 Figure 2.11: Proteome comparison of 32 Vibrionaceae genomes. Environmental V. cholerae strains lacking the cholera enterotoxin genes are highlighted in bright green, whilst pathogenic V. cholerae strains genomes are shown in dark green. Large similarities between environmental and pathogenic V. cholerae The BLAST matrix shown in figure 2.11 includes environmental and pathogenetic strains of V. cholerae. The figures shows that within and between these two groups the V. cholerae strains share a large number of genes. Intra- vs. inter-proteome similarity The lower row of the diagram shows the special case of organism A versus itself. This shows the intra-proteome similarity. If not dealt with separately, this part would appear as 100% similar since the proteome is BLASTed against itself. However, all self-matching proteins are excluded, leaving this part to reflect the paraloges of the organism. Also, this part has a separate color encoding (red) whereas the intra-protome comparison is coded green (see figure 2.10). 2.3.7 BLASTatlas - visualizing while-genome homology The BLASTmatrix tool described earlier condenses the similarity between two proteomes into a single number. This simplification allows for an all-against-all comparison, but lacks detailed information on the conserved genes and where these are located. The BLASTatlas method overcomes these issues by comparing the proteomes to a single reference chromosome. When a single representative chromosome has been selected, all ORF’s or proteins of that reference is BLASTed against each of the proteome to be included in the comparison. The most optimal alignment of each proteome, disregarding the significance, is mapped back to the reference genome. A numerical value of zero is mapped at mismatches or gaps, 0.5 at conservative mismatches, and one is mapped to matches. This method has proved powerful because it answers several questions in one diagram: Which reference proteins are found in which query genomes? How well are they conserved? And is there 18
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phylogenies based on alternative ho
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Table 2 A selection of genes locate
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4314 74 Tools Abstract: Of the plet
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Chapter 3 rRNA operons and promoter
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Using HMMs also simplifies the use
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of the annotation. Some of the majo
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synthesis in flow cells to simultan
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Read absence. A boolean where ‘on
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Hallin, et al. Figure 4 | The dataf
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Genome homology: Comparing multiple
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ing platform-‐independent Java
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34. Wang H, Noordewier M, Benham CJ
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Chapter 4 Web Services and Interope
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Web Services and Interoperability i
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Chapter 5 Conclusion and perspectiv
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Appendix A Appendix: Workshops, tea
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Appendix B Appendix: Ph.D. study pl
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Danmarks Tekniske Universitet AFI,
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Danmarks Tekniske Universitet AFI,
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Appendix C Appendix: Courses C.1 Gl
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D.2 Sample output from queryGenomes
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Appendix: Software 13 w a r n " $ o
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Appendix: Software 109 m y ( $ m i
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Appendix: Software 25 [ ] A l t e r
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BIBLIOGRAPHY J. Rogers, P. F. Stadl
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BIBLIOGRAPHY Q. Jin, Z. Yuan, J. Xu
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BIBLIOGRAPHY Velicer, F.-J. Vorholt
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