exim is a program that compares two time-series expression profiles using the dynamic programming algorithm. To avoid bias due to differences in magnitudes, the vectors are first normalized such that each has zero mean and standard deviation of one. Unlike sequence comparison, gaps are not allowed, since the meaning of a gap is that a time delay is introduced. If two genes are co-expressed (possibly with a time-shift) it is unlikely that one will re-synchronize itself to the other, once they departed (a gap was introduced).
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