Motif FindingAlignACE(Aligns nucleic Acid Conserved Elements)

• Modification of Gibbs Motif Sampling (GMS), a routine for motif finding in protein sequences (Lawrence, et al. Science 262:208-214, 1993).

• Advantages of GMS:
  • stochastic sampling
  • variable number of sites per input sequence
  • distributed information content per motif

• AlignACE modifications:
  • considers both strands of DNA simultaneously
  • efficiently returns multiple distinct motifs
  • various other tweaks

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