Genome-wide predictability of restriction sites across the eukaryotic tree of life

The software developed is available in this page. This software will help guide the design of any study using RAD sequencing and related methods.

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Requirements

• Python 2.7 and above
• Biopython
• Bowtie

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Install

Download python and shell scritps

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Usage

• pattern_for_genome.sh. This shell script will search all the restriction sites from the input file (patternfilename) in every genome from the input file (genomefilename). As a result this scripts creates

  The input arguments are are:

  • genomefilename: name of file with table with two columns (1) species code and (2) link to whole genome fasta file (see example/test_pattern_for_genome/example_genome_table )

  • patternfilename - name of file with table with tow columns (1) restriction site regular expression and (2) restriction site name (see example/test_pattern_for_genome/patternfilename)

  To run, just write on shell

  patternforgenome.sh genomefilename patternfilename

• genome_nucleotide_distrib.py.

  The input files are:

  • genomefilename
  • resultsfile

  To run, just write on shell

  python genomenucleotidedistrib.py genomefilename resultsfile

• sequence_probability.py

  To run, just write on shell

  python sequenceprobability.py distributionfile patternsfile