Software for filling the scaffold

Introduction

• Input: completeGenome.txt and genomeInScaffold.txt.

  As in the sample test data here, the format for input files:

  1. Each line represents a scaffold, and there is at least one space between two successive genes.
  2. A gene name can be any string without spaces. A default Ò+Óis understood for all the genes on one of the strands, but an explicit Ò-Ò sign must be added to all genes located on the other strand.
  3. In genomeInScaffold.txt file, we use ÒgapÓ to represent a gap into which missing genes can be inserted. In addition there are implicit gaps at the beginning and end off each scaffold, and ÒgapÓ need not, and in fact should not, be written there.
• Output:
  1. The DCJ distance between these two genomes after scaffold filling.
  2. The genomeInScaffold after scaffold filling.
• To run the program:
  1. Download and unzip the zipped file here
  2. Direct the terminal to the folder scaffoldFilling, which contains the java script
  3. Run the program:

     java Test completeGenome.txt genomeInScaffold.txt > result.txt

  4. Check the output in the result.txt file

• To test other sets of genomes
1. Copy yourCompleteGenome.txt and yourGenomeInScaffold.txt to the scaffoldFilling folder.
2. Run the program again with your input files:

   java Test yourCompleteGenome.txt yourGenomeInScaffold.txt > yourResult.txt