COMPAM : How to get Data

· Making the inputs of comapm

1. Run blastz for all pairs of genomes: all_pair_blast.pl

To run this script, you should be copy or move sequence files (*.fna) to a directory.

> all_pair_blast.pl -i test

The above command will compare all pairs of the files in the directory 'test' and store the ouput files of blastz to 'test'.

2. Generation of input files of compam

Compam uses various file formats:

raw seqeunce file (accession.fna.out),

gene location file (accession.gbk.genelctn),

match information file (Ref_Genome.accession),

region information file (region.accession.accession),

To make the input files of compam, you should copy or move annotation files (*.gbk and *.ptt) in the same directory stored sequence files (*.fna) and blastz output files(*.*.blastz), say 'test'.

> compam_input -i test

The above command will make all files needed by compam from various files.

Example>

We wanna to use three genomes: NC_000908, NC_000912, NC_002950

> ls test

NC_000908.fna NC_000908.gbk NC_000908.ptt NC_000912.fna NC_000912.gbk NC_000912.ptt NC_002950.fna NC_002950.gbk NC_002950.ptt

> all_pair_blast.pl -i test

> ls test

NC_000908.fna NC_000908.NC_000912.blastz NC_000908.ptt NC_000912.gbk NC_000912.ptt NC_002950.gbk

NC_000908.gbk NC_000908.NC_002950.blastz NC_000912.fna NC_000912.NC_002950.blastz NC_002950.fna NC_002950.ptt

> compam_input.pl -i test

> ls test

NC_000908.fna NC_000908.ptt NC_000912.ptt Ref_Genome.NC_000908 region.000908.002950

NC_000908.fna.out NC_000912.fna NC_002950.fna Ref_Genome.NC_000908.sorted region.000912.000908

NC_000908.gbk NC_000912.fna.out NC_002950.fna.out Ref_Genome.NC_000912 region.000912.002950

NC_000908.gbk.genelctn NC_000912.gbk NC_002950.gbk Ref_Genome.NC_000912.sorted region.002950.000908

NC_000908.histogram NC_000912.gbk.genelctn NC_002950.gbk.genelctn Ref_Genome.NC_002950 region.002950.000912

NC_000908.NC_000912.blastz NC_000912.histogram NC_002950.histogram Ref_Genome.NC_002950.sorted

NC_000908.NC_002950.blastz NC_000912.NC_002950.blastz NC_002950.ptt region.000908.000912

> java -jar compam.jar

· How to download the data on the web

1. Select data(genome and sequence) on the COMPAM web server.

2. Click data download file between progress bar and applet view.

3. Install the data on the data directory COMPAM is working.

      In this case, you should delete all data files which you used previous processing.