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CompariMotif Relationships
CompariMotif Match Type Examples. See text below for details.
The best match is then considered to define the relationship between the two motifs. (See How CompariMotif works.) These relationships are comprised of the following keywords:
- Match type keywords identify the type of relationship seen:
- Exact = all the matches in the two motifs are precise
- Variant = the focal motif contains only exact matches and subvariants of degenerate positions compared to the other motif
- Degenerate = the focal motif contains only exact matches and degenerate versions of positions in the other motif
- Complex = some positions in the focal motif are degenerate versions of positions in the compared motif, while others are subvariants of degenerate positions
- Match length keywords identify the length relationships of the two motifs:
- Match = both motifs are the same length and match across their entire length
- Parent = the focal motif is longer and entirely contains the compared motif
- Subsequence = the focal motif is shorter and entirely contained within the compared motif
- Overlap = neither motif is entirely contained within the other
This gives sixteen possible classifications for each motif's relationship to the compared motif. (See below for examples.)
Example Match Types
Examples for each of the sixteen match types are shown above. In each case, the "query" motif [KR]xLx[FYLIMVP] is compared to an invented motif for illustration. Because of the natural relationship between parent/subsequence and variant/degenerate matches, these have been grouped in the figure. Matched positions that contribute towards the number of matched positions (i.e. those not involving a wildcard position) are marked with an asterisk.
- Exact Match: All positions are identical and the match spans the full length of both motifs.
- Variant/Degenerate Match: The match spans the full length of both motifs. All of the positions of the query are either the same as the match (X v. X and L v. L) or more degenerate ([KR] v. R, X v. P & [FYLIMVP] v. L) and so it is classed degenerate. Likewise, all positions in the other motif, RxLPL, are either identical to the query or variants of the query positions, so it is classed as variant.
- Complex Match: Again, the match spans the full length of both motifs. This time, each motif has some positions that are more degenerate than in the other motif. i.e. The query is a variant for the L v. X position but more degenerate at all other positions.
- Exact Parent/Subsequence: The [KR]xL motif is entirely and exactly contained within the query.
- Degenerate Parent/Variant Subsequence: The RxLE motif is entirely contained within the query. At two positions, however, ([KR] v. R & X v. E) the query is more degenerate and is hence a "degenerate parent", while RxLE is a "variant subsequence".
- Variant Parent/Degenerate Subsequence: This time it is the query that is the variant in one position (L v. IL) and so the variant/degenerate labels are swapped.
- Complex parent/subsequence: the L[IL]xL motif is less degenerate at two positions (X v. L & [FYLIMVP] v. L) but more degenerate at one (L v. [IL]) and so the relationship is "complex".
- Exact overlap: Neither motif is entirely contained within the other but the positions overlapping match exactly.
- Degenerate/variant overlap: Neither motif is entirely contained within the other. The first P of LxPP is a variant of the [FYLIMVP] in the query, while the other two matches (an L and an X) are exact, therefore the query is "degenerate" and LxPP is "variant".
- Complex overlap: Neither motif is entirely contained within the other and both contain positions that are degenerate when compared to the matching position in the other motif ([KR] v. R & X v. S are degenerate in the query, L v. [ILMV] is degenerate in RxRS[ILMV]).