Quick phage comparison

A quick comparison of a phage genome against all phage genomes

 perl ~/Documents/scripts/run_mash_phage_get_species_JUL18.pl input.fasta

This will compare your phage genome against a database of complete phage genomes using MASH. READ the docs to make sure you know what MASH does. The database is constructed from the monthly download of phage genomes from Genbank. The sketches are precomputed at -s 1000. The output is to screen and produces tab format of


To redirect to the output to a  file use

 perl ~/Documents/scripts/run_mash_phage_get_species_JUL18.pl input.fasta >MASH_output.txt

To estimate similarity then 1-Distance(*100) is ~ ANI

MUMMER to compare two genomes
Read the manual so you can work out what the script does

 perl ~/Documents/scripts/run_nucmer.pl file1.fa file2.fa

You will get a number of output files. Use

 display out.png

To display the ouput of the alignment, which will look like below

All current phage genomes are in /blastdb/Bacteriophage_genomes see http://millardlab.org/bioinformatics/lab_server/ for details of the database.
WARNING the script overwrites existing files of the same name.

For comparing multiple phage genomes at a time use

perl ~/Documents/scripts/run_nucmer_multiple_genomes.pl

or if you wish to use promer then

perl ~/Documents/scripts/run_promer.pl