Below is an example output file converted from postscript to gif so the resolution isn't great. This is the output from a BLASTN search using the mitochondrial cox1 intron present in some groups and 50bp of the cox1 gene flanking the intron. Groups that contain the intron within the cox1 gene are the top hits. Other taxa that contain introns with lower similarity are shown next in violet and cox1 genes that lack the intron can be seen by the two green flanking regions.


If the first HSP of a database hit has an expectation value less than or equal to the expectation-cutoff, all the HSPs in the blast output for this database sequences are represented relative to where they match the query sequence.

All HSPs for a database hit are displayed on the same line. The height of the line is proportional to the percent identity by the following relationship:


The HSPs are colored as in the NCBI graphical output by bit scores.


  1. download the latest release => here
  2. tar zxvf blast2psVERSION.tar.gz
  3. cd blast2ps
  4. ./blast2ps blast-output-file expectation-cutoff >
  5. you can copy blast2ps to somewhere in your path (eg. /usr/local/bin) if you'd like.

Danny Rice
Last modified: Wed May 17 15:57:40 EDT 2006