  Background
  Nucleotide sequences contain multiple codes responsible for organism's
functioning and structure. They can be investigated by various signal
processing methods. These techniques are well suited for indication of
frequently encountered sequence motifs (i.e., repeats). However, if there are
two or more codes containing the same motif, the local nucleotide distribution
(i.e., profile), resulting from sequence alignment by the motif position, will
represent overlapping of the code patterns.
  Results
  The novel algorithm for decomposition of pattern overlapping is proposed. It
is capable to work with dispersed repeats as well. The algorithm is based on
cross-correlation procedure applied locally in a cumulative fashion. Its
sensitivity was tested on human genomic sequences.
  Conclusions
  Cumulative Local Cross-Correlation was successfully used to decompose
overlapping of nucleotide patterns in human genomic sequences. Being very
general technique (as general as cross-correlation), it can be easily adopted
in other signal processing applications and naturally extended for
multidimensional cases.
  Software implementation of the algorithm is available on request from the
authors.
