Statistical properties of nucleotide clusters in DNA sequences

Statistical properties of DNA sequences.

We review evidence supporting the idea that the DNA sequence in genes containing non-coding regions is correlated, and that the correlation is remarkably long range--indeed, nucleotides thousands of base pairs distant are correlated. We do not find such a long-range correlation in the coding regions of the gene. We resolve the problem of the "non-stationarity" feature of the sequence of base pa...

Nucleotide sequences in DNA

Statistical analysis of nucleotide sequences.

In order to scan nucleic acid databases for potentially relevant but as yet unknown signals, we have developed an improved statistical model for pattern analysis of nucleic acid sequences by modifying previous methods based on Markov chains. We demonstrate the importance of selecting the appropriate parameters in order for the method to function at all. The model allows the simultaneous analysi...

Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences.

The human genome encodes the transcriptional control of its genes in clusters of cis-elements that constitute enhancers, silencers and promoter signals. The sequence motifs of individual cis- elements are usually too short and degenerate for confident detection. In most cases, the requirements for organization of cis-elements within these clusters are poorly understood. Therefore, we have devel...

Determination of nucleotide sequences in DNA.

In spite of the important role played by DNA sequences in living matter, it is only relatively recently that general methods for their determination have been developed. This is mainly because of the very large size of DNA molecules, the smallest being those of the simple bacteriophages such as qXl74 (which contains about 5,000 nucleotides). It was therefore difficult to develop methods with su...