Figure 2.

Composite sequence alignment. This is one of the methods for viewing the results of queries. This query retrieved sequences from HIV-1 subtype B patients receiving nelfinavir as their sole protease inhibitor. The page header shows the query parameters and the numbers of references, patients and isolates returned by the query. The figure legend shows whether the user wished to view the absolute number of mutations at each position and whether the user wished to ignore rare occurrences that were observed in only one sequence. The first line in that summary shows the numbered consensus sequence. The second line contains the total number of isolates in the data set at each position. The remaining lines show the frequency of variation at each position in the sequence data set. If this composite alignment is compared to the composite alignment of protease sequences from untreated patients, one would observe that the changes at codons 30, 46, 73, 88 and 90 occurred only in isolates from patients who had received nelfinavir and that changes at codons 36 and 71 were present in both alignments but occurred more commonly in isolates from patients receiving nelfinavir.