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Download

repDNA-1.1.4.zip -- The source Zip file for installing the repDNA package on Windows, Linux, Unix, Mac OS

Quick to start

repDNA_manual.pdf for how to use repDNA, and the descriptions of the 15 features in the package.
repDNA_example.pdf includes some examples of how to construct computational predictors for three tasks in computational genomics by using repDNA.

Datasets and Python scripts used in the three examples in Online Supporting Information S2 (repDNA_example.pdf)

Tasks Positive dataset Negative dataset Python script
DNasel HS prediction hs.fasta non-hs.fasta example1.py
Nucleosome positioning prediction H_sapiens_pos.fasta H_sapiens_neg.fasta example2.py
Recombination spot identification hotspots.fasta coldspots.fasta example3.py
repDNA_example.zip contains all the files shown in this table.

Values of the physicochemical indices

38_dinucleotide_physicochemical_indices.zip
-- the 38 physicochemical indices for dinucleotides shown in Table 1 in Online Supporting Information S1.
12_trinucleotide_physicochemical_indices.zip
-- the 12 physicochemical indices for trinucleotides shown in Table 2 in Online Supporting Information S1.
6_dinucleotide_physicochemical_indices.zip
-- the 6 physicochemical indices for dinucleotides shown in Table 3 in Online Supporting Information S1.