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Like Blast Score Ratio (BSR)

Case of use for Find_Genomic_Islands for Vibrio parahaemolyticus

These script find genomic islands (GIs) that may play a role in the emergence and pathogenesis of pandemic strains. Predicted Genes with prodigal in draft assembly genomes and return a Matrix.tab with Blast score ratio for each gene in your draft genome.

The concept of the BSR you can review these paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC545078/)

Usage:

    $ python3 like_bsr.py dir_DraftGenomes Multifasta_for_DB/*fasta #cores name_output

dir_DraftGenomes = Directory with your draft genomes or complete genomes

Multifasta_for_DB = A file multifasta with genes of your interest. check - dir_multifasta

Dependences

You need install all programs in your environmetal path. See instructions for each case:

  1. python3 and libraries seaborn, numpy, dataframe.
  2. BLAST ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
  3. Prodigal https://github.com/hyattpd/Prodigal