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Information about computing options.
EXPLORE: sequence similarities exploration.
The EXPLORE procedure
analyses the global similarity between the whole set of
sequences. The frequency distribution of the similarity between all residue
segments is compared to the one obtained after shuffling the sequences. If at
least two sequences in the set are not significantly similar, reliability of
the procedure ALIGN may be affected. A similarity matrix between sequences is
computed and, for more than four sequences, treated by a principal component
analysis.
ALIGN: optimal alignment computation.
The ALIGN procedure matches the most similar 9-residue segments in a scan
of the whole set of sequences. The similarity between segments is defined from
the selected scoring matrix and is limited by a statistical threshold. Only
complete matches are retained; a complete match is a set of segments, selected
in all the sequences, in which each segment is similar to all the other
segments.
The complete matches are then arranged in regions not disrupted by gaps
("boxes") and assembled in an alignment. The gaps are allocated arbitrarily
before each box.
Four steps of matching are performed successively with a decreasing
statistical significance in order to fix reliable anchor points at the
beginning and to enlarge them in the next steps.
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