Instructions for

This script parses the xml output file from NCBI's Blastn program and calculates average error rates of different types (insertion, deletion, substitution).


  1. Blastn output xml file.
  2. Cutoff value for fraction of query sequence that aligned to subject sequence (0-1). The alignment that fraction is below the cutoff is considered as randomly. The default value is 0.6.


  1. Stats file of calculated three types of error rates.
  2. Optional pairwise alignment file of each query aligned to reference and the counts of insertions, deletions and substitutions.

How to run

  1. Download to your local computer, and set it as executable by typing the following command in your working directory:

    chmod +x

  2. Create a subdirectory in your working directory to hold input files and output files. In the subdirectory, type following command:

    perl ../ blastXmlOutFile outputStatsFile alignFractionCutoff pairwiseAlignFile(optional)