Usage

• See the pre-built demonstration here.
  • Right-click and drag to rotate, alt-drag to zoom in/out, shift-drag to pan
• First, download dna/rna sequences, such as the ones from UCSC, here
  • Create a directory storing the uncompressed files in .fa format
  • There will be one file per chromosome.
  • If necessary, rename the files to have names like chr1.fa, chr2.fa, etc.
• Then, download the source code see-across-chrom-0.2.tar.gz
  • Windows/msvc
    • Compile code
    • Open console, cd to path containing see_chrom_regions.exe
    • Type set CHROM_DNA_PATH=/path/to/directory to point to directory with chr1.fa.
    • Type set CHROM_CHROMS_TO_DO=3 where 3 is the number of .fa files you want to analyze.
    • Type .\see_chrom_regions.exe to run the tool
  • Linux
    • Open console, cd to path
    • Type make to compile
    • Type export CHROM_DNA_PATH=/path/to/directory to point to directory with chr1.fa.
    • Type export CHROM_CHROMS_TO_DO=3 where 3 is the number of .fa files you want to analyze.
    • Type ./see_chrom_regions to run the tool
  • Choose option 1 and wait until the tool completes.
  • Make note of where out.glowscript is stored.
• Go to glowscript.org
  • Sign up for an account (instantaneous)
  • Create a 'new program'
  • Copy/paste the contents of out.glowscript into the box in your browser
  • Click Run Program and the visualization should be there!
  • Right-click and drag to rotate, alt-drag to zoom in/out, shift-drag to pan

More possibilities:

• Environment Variable settings
  • CHROM_CHROMS_TO_DO
    • If set to 3, only processes chr1.fa to chr3.fa.
  • CHROM_NTHREADS
    • Number of threads. Default is 4.
  • CHROM_NCONNECTIONS
    • Number of lines to draw in visualization.
  • CHROM_REGION_LENGTH
    • Size of region, defaults to about 1 million bases.
  • CHROM_NUM_BUCKETS_KEPT
    • By default we only consider the 1600 most-occuring dna sequences.
• Connections are currently drawn such that red lines are more similar and gray lines are less similar. To see all connections simultaneously, edit the glowscript file,
  • Change the line cv.visible = c1 == current_highlight or c2 == current_highlight to be cv.visible = True
  • You're encouraged to make further changes and improvements to the glowscript file.
• Distance scores are stored in a sqlite database, for further investigation. You can use a sqlite browser tool to view the similarities data.