Compositional representation of protein sequences and the number of Eulerian loops

Details Compositional representation of protein sequences and the number of Eulerian loops Compositional representation of protein sequences and the number of Eulerian loops

2001-03-10

arxiv.org/abs/physics/0103028v1

Physics

Biological Physics

5 pages, no figure, 2 tables, RevTex3.1

Scientific paper

An amino acid sequence of a protein may be decomposed into consecutive overlapping strings of length K. How unique is the converse, i.e., reconstruction of amino acid sequences using the set of K-strings obtained in the decomposition? This problem may be transformed into the problem of counting the number of Eulerian loops in an Euler graph, though the well-known formula must be modified. By exhaustive enumeration and by using the modified formula we show that the reconstruction is unique at K equal or greater than 5 for an overwhelming majority of the proteins in the PDB.seq database. The corresponding Euler graphs provide a means to study the structure of repeated segments in protein sequences.

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