A fast algorithm for counting the arrangements for packing identical items on a one-dimensional grid with application in DNA-protein and similar interactions.
An algorithm is described, originally developed for use with DNA-protein complexes, which precisely counts the number of possible arrangements for non-overlapping items, each occupying M points, on a lattice of N such points. The algorithm counts the total number of arrangements for a given number of items and can be readily extended to count the number of arrangements which meet an additional criterion. Examples are given of two such classifications and of the application of one of them to a problem in DNA-protein interactions.
Badcoe
I G
IG
Molecular Recognition Centre, Department of Biochemistry, University of Bristol Medical School, University Walk, UK.
D000465:Algorithms; D004247:DNA / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000378:metabolism*; D008432:Mathematical Computing; D008956:Models, Chemical
D004268:DNA-Binding Proteins; D004247:DNA