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Figure 4 | Algorithms for Molecular Biology

Figure 4

From: Stability of multiple alignments and phylogenetic trees: an analysis of ABC-transporter proteins family

Figure 4

For most alignment algorithms, sequence duplications can lead to serious mis-alignments and to instabilities under minor modifications of the input sequence sets. For our original sequence set = {S 1, ..., S 22} and the 'reduced' sequence sets i := \{Si}, we obtained six classes of multi-alignments. Here, class 3 and 5 seem to be the only types of alignments that are biologically meaningful. Alignments of class 5 were obtained only once, namely by DIALIGN using the xfr option as described in 2 and 4.3. We used this option to prevent the program from aligning the motifs A2, S2 and B2 in the sequences S20 – S22 to the motifs A, S and B in the remaining sequences.

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