Single-base resolution nucleosome mapping on DNA sequences.
Nucleosome DNA bendability pattern extracted from large nucleosome DNA database of C. elegans is used for construction of full length (116 dinucleotide positions) nucleosome DNA bendability matrix. The matrix can be used for sequence-directed mapping of the nucleosomes on the sequences. Several alternative positions for a given nucleosome are typically predicted, separated by multiples of nucleosome DNA period. The corresponding computer program is successfully tested on best known experimental examples of accurately positioned nucleosomes. The uncertainty of the computational mapping is +/-1 base. The procedure is placed on publicly accessible server and can be applied to any DNA sequence of interest.
Gabdank
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Department of Computer Science, Ben Gurion University of the Negev, P.O.B 653 Be'er Sheva 84105, Israel. gabdank@cs.bgu.ac.il
Barash
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Trifonov
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D000818:Animals; D001483:Base Sequence; D017173:Caenorhabditis elegans / Q000235:genetics; D002843:Chromatin / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D002874:Chromosome Mapping / Q000379:methods*; D030561:Databases, Nucleic Acid; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009707:Nucleosomes / Q000737:chemistry* / Q000235:genetics*
D002843:Chromatin; D009707:Nucleosomes