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Jumping ALIgnments

Computes Jumping ALIgnments from a protein sequence and an alignment of a protein family.

INPUT :: Sequence

Protein sequence

INPUT :: Alignment

Alignment of a protein family

OUTPUT :: Jumping Alignment

Jumping alignment computes from protein sequence and an alignment of a protein family.

Parameter

Name Description
gap initiation Gap initiation cost
gap extension Gap extension cost
jump Jump cost
similarity matrix amino acid similarity matrix
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