Biology Reference
In-Depth Information
Fig. 4 Examples of dot plot. (a) Screenshot of dot plots in MAFFT service; (b-d) individual plots; (b) comparison
of identical sequence;
(c) no obvious large-scale genomic rearrangements;
(d) reverse complementary
sequences; (e) one large inversion; MAFFT cannot be applied to e
instead of MAFFT. Even if MAFFT returns an MSA for such a
problem, the MSA is inappropriate for the region shown in blue in
this plot.
5
Estimating the Direction of DNA Sequences
In the case of nucleotide alignments, if some of the input sequences
have an entirely opposite direction to the other sequences, the
directions can be automatically adjusted by the
--adjustdirec-
tion
option. This option is also available on the web version, with
the “Adjust direction” button. There are several possible natural
methods to determine the direction of nucleotide sequences.
Most naively, the direction of sequences can be estimated by
comparing the first sequence and the other sequence with both
forward and reverse directions. If the similarity score of forward-
forward comparison is worse than that of forward-reverse compari-
son, the sequence is judged to have the opposite direction to the first
sequence and its reverse complement replaces the sequence. This
strategy works well in most cases, but, when the first sequence is
phylogenetically isolated in the input data, the difference in
