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Dot plots are a very simple method to visualize regions of
similarity between two sequences. The sequences are placed
on the horizontal and vertical axis, respectively. For each position
in the diagram, a dot is drawn if the two characters in the
sequences are identical at the corresponding positions. Adjacent regions of
identity give rise to diagonal lines in the plot.
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Global (Needleman-Wunsch) alignments
assume that two sequences are similar over their
entire length. The alignment attempts to match the sequences from
end to end, even if parts of them are not similar.
EMBOSS
( European Molecular Biology Open
Source Software Suite) [ Rice et al.
2000] is a
free open source software package for sequence
analysis. It includes needle, a tool for global alignments.
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Local (Smith-Waterman) alignments search
for segments of two sequences that are similar. Only those parts of
the sequences that have good matches according to some criterion are
aligned.
water is the EMBOSS tool for local alignments.
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