DNA curvature

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DNA curvature
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Complete sequence of HIV 1
Nucleotide
HIV-1organism complete genome
http//www.ncbi.nlm.nih.gov/
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Savig the data
Save data to file
From GBK format to FASTA
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Map computation
Sintaxis of the program curvature -f
AY255828.fast -o AY255828.crv100.out -m 100 -f
input file -o output file -m size of the window
Sorting of the output data sort -r -n -k 2 k 2
second column, n numeric data, r revers index
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Visualisation of the curvature map
Plotter xmgr - peaks of curvature maximally
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Filtering of the data
Nawk if(2gt0.2) print 0 input gt output The
output data is formed clusters It is need to take
only some peaks
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Path computation
http//research.haifa.ac.il/genom/Alex's_page/ind
ex.html
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Curvature software
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Input data
To take sequences length 2-3 size of window
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3D structure of DNA