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Updated: Jun 25, 2026

Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules
Published on: April 12, 2019
Counting of oligomers in sequences generated by markov chains for DNA motif discovery
1Beijing Genomics Institute, Shenzhen (BGI-SZ), Shenzhen 518083, China.
Abstract:
By means of the technique of the imbedded Markov chain, an efficient algorithm is proposed to exactly calculate first, second moments of word counts and the probability for a word to occur at least once in random texts generated by a Markov chain. A generating function is introduced directly from the imbedded Markov chain to derive asymptotic approximations for the problem. Two Z-scores, one based on the number of sequences with hits and the other on the total number of word hits in a set of sequences, are examined for discovery of motifs on a set of promoter sequences extracted from A. thaliana genome. Source code is available at http://www.itp.ac.cn/zheng/oligo.c.
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