Computational tools and Interoperability in Comparative ... - CBS

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
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