Template:GlycosidicBondComparisonText

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Glycosidic Bond Comparison

Each specific characteristic of the aligned glycosidic bonds attaching a child monosaccharide to a parent monosaccharides are considered to be sets. Missing characteristics represent a set containing all possible values. For a strict alignment, glycan glycosidic bond characteristics must be contained in (or, a subset of) the corresponding glycosidic bond monosaccharide characteristics. For a non-strict alignment, glycan glycosidic bond characteristics must have an non-empty intersection with the corresponding motif glycosidic bond characteristics.

Since linkage type and child linkage position typically are either specified with a single value or are missing, we can simplify the above statements as follows:

For a strict alignment, aligned motif and glycan glycosidic bonds attaching a child monosaccharide to a parent monosaccharide must:

1a. have the same child linkage type (n,d,...), if the motif glycosidic bond child linkage type is specified; and

2a. have the same child linkage position (1,2,...), if the motif glycosidic bond child linkage position is specified; and

3a. have the same parent linkage type (d,o,...), if the motif glycosidic bond parent linkage type is specified; and

4a. have the glycan parent linkage positions (2,3,4,5,6,...) be a subset of the motif glycosidic bond parent linkage position.

For a non-strict alignment, aligned motif and glycan glycosidic bonds attaching a child monosaccharide to a parent monosaccharide must:

1b. have the same child linkage type (n,d,...), if the motif and glycan glycosidic bond child linkage type are specified; and

2b. have the same child linkage position (1,2,...), if the motif glycosidic bond child linkage position are specified; and

3b. have the same parent linkage type (d,o,...), if the motif glycosidic bond parent linkage type are specified; and

4b. have the glycan parent linkage positions (2,3,4,5,6,...) have non-empty intersection with the motif glycosidic bond parent linkage positions.

Motif Linkage Structure Linkage Alignment?

o(3+1)d

o(3+1)d

Yes, strict alignment. Identical linkages.

o(-1+1)d

o(3+1)d

Yes, strict alignment. All linkage properties specified in the motif linkage contain the properties in the glycan linkage.

o(3+1)d

o(3+-1)d

Yes, non-strict alignment. Glycan child linkage positions have non-empty intersection with motif child linkage positions.

o(2+1)d

o(2|4+1)d

Yes, non-strict alignment. Glycan parent linkage positions have non-empty intersection with motif parent linkage positions.

o(2+1)d

o(-1+1)d

Yes, non-strict alignment. Glycan parent linkage positions have non-empty intersection with motif parent linkage positions.

o(4|6+1)d

o(2|4+1)d

Yes, non-strict alignment. Glycan parent linkage positions have non-empty intersection with motif parent linkage positions.

o(-1+1)d

o(2|4+1)d

Yes, strict alignment. Glycan parent linkage positions are contained in the motif parent linkage positions.