Breakpoint Detection Using Partially Local Alignments

1. System requirements/Installation

BrpAln sources are written in c++ and one python script to output the alignment file stockholm format.



tar -zxvf BrpAli.tar.gz

Build BrpAli.cpp:

g++  -O3  BrpAli.cpp -o BrpAli


./BrpAli [options] 

System requirements:

  • Linux operation system.

  • g++ compiler.

  • Python 2.7 and biopython.

2. Required running options

  • -m Match score.

  • -u Mismatch score.

  • -g Gap score.

  • -s Sum of pairs weight in the 3-D alignment.

  • -i Input file in fasta format.

  • -o Output file.

  • -f Output alignment format <sto/fas> for stockholm or fasta

3. Input file

  • Fasta format.
  • Contains three sequences: Reference (F), left (L) and right (R).
    • F Last segment of the left reference gene + intergenic region + first segment of right refernce gene.
    • L Last segment of the left query gene.
    • R First segment of the right query gene.
The three input sequences.

The three input sequences.

For more info or reporting problems please contact