Genome Comparison Map generator (GCM.exe) is an executable command-line Perl script that generates Genome comparison maps.

The GCM program completely automates following processes :

• Installation and configuration of BLAST server locally
• Performing BLAST search on multiple genomes.
• Post-processing BLAST results of each genome compared, to generate:
  • A tab delimited file containing BLAST results in an easy to ready format.
  • Several HTML files each containing sequence-specific BLAST alignments.
• Generating interactive comparison maps in two varieties:
  • Standalone
  • Web-based

The tool itself has inbuilt BLAST server, on a Windows system no other software is needed to run GCM prorgam.

Graphics are created as SVG (Scalable Vector Graphics) files. Click here to download SVG Plug-in for Windows

Genome Comparison Maps generated by GCM program are scalable,searchable,and highly interactive.

NOTE: THIS PROGRAM TESTED WITH BACTERIAL GENOMES ON WINDOWS ENVIRONMENT ONLY.

The figure below (Figure 1) is a GCM generated comparison map displaying the relationships of Lawsonia intracellularis PHE/MN1-00 genome with other 11 bacterial genomes:

Figure 1: Lawsonia intracellularis PHE/MN1-00 genome comparison map

The figure below (Figure 2) is a GCM generated comparison map displaying the relationships of Mycobacterium avium subsp. paratuberculosis K-10 genome (5324 proteins) with 15 bacterial genomes

Figure 2: Mycobacterium avium subsp. paratuberculosis K-10 genome comparison map.

Query genomes feature-specific Information is displayed (Figure 3) as a pop-up menu (when user mouse-over) displaying following information and dynamic links to external resources:

• Query proteins: Synonym
• Start - Stop coordinates
• Protein name and description
• COG group description
• HTTP link to NCBI GenBank record
• HTTP link to KEGG pathways
• HTTP link to sequence (FASTA format)
• HTTP link to PubMed Search

Figure 3: Query genome popup box

On passing the mouse over on a BLAST result rectangle, a popup link menu is displayed (Figure 4) with the following information:

• Subject genomes matching proteins:
• Synonym (locus tag id)
• HTTP link to NCBI GenBank record
• HTTP link to sequence (FASTA format)
• Description of percent identity with query protein sequence
• HTTP link to view the actual BLAST alignment

Figure 4: Subject genome popup box

Figure 5: Web-based genome comparison map of Chlamydia muridarum Nigg.

DOWNLOAD:

• This script uses "% IDENTITY" as a refercen for SIMILARITY
• This script uses "BLAST SCORE" as a refercen for SIMILARITY

Note: If you are downloading the both versions, then please store and run them from different folders

In both scripts users can assign thier own colours OR use standard colours:

• Standard colours for % IDENTITY:
  • >=80% Identity----------------->bisque
  • >=60% & <80%Identity-------->pink
  • >=40% & <60%Identity--------> green
  • >=20% & <40%Identity--------> grey
  • <20%Identity-------------------> blue
    
• Standard colours for BLAST SCORE:
  • >=200 score--------------->red
  • >=80&<200 score--------->violet
  • >=50&<80 score---------->green
  • >=40&<50 score---------->blue
  • <40 score----------------->black

   

GCM USAGE:

GCM command line options:

[-QC S|C] [-SC SCC|UDC] [-E num] [-O S|W] [-QF query FAA file] [-QP query PTT file] [-SF subject1 FAA file, subject2 FAA File, so on]

‘or'

–h for help

Example option: -QC S -SC SCC -E 0.5 -O W -QF NC_004552.faa -QP NC_004552.ptt -SF NC_002179.faa,NC_007514.faa

Option QC (Query Genome Colour option): This option allows the user to choose one of the following options to colour gene products on the comparison map:

• Option S (Standard): to use standard colours: ‘Red' for reverse and ‘blue' for forward strand.
• Option C (COG): to colour gene products according to their clusters of orthologous groups. If COG's information is not available, GCM automatically uses standard colour option. (Please see chapter 4: Table 4.3 for COG based colour table details)

Option SC (Subject Genomes Colour option): Users can specify their choice of colours or use standard colours to display different sequence identity levels on comparison map.

• Option SCC (Standard colours for comparison)
• Option UDC (User defined colours): Choosing this option allows the user to configure different colours to display subject genomes BLAST results. A compiled list of SVG colours can be found at: www.december.com/html/spec/colorsvg.html

Option E (Expectation value): This option allows the user to set an expectation value for BLAST search. The “E” value is a measure of the reliability of the “S” score, where ‘S' score is a measure of the similarity of the query to the resulting sequence. Choosing the lower E value will give much more significant results.

Option QF (Query genome FAA file): This option is used for inputting the BLAST search query genome FAA (Amino acid sequences in FASTA format, e.g. NC_004552.faa) file.

Option PT (Query genome PTT file): This option is used for inputting the query genome protein table (PTT) file (e.g.NC_004552.ptt). The GCM uses protein coordinate information from PTT file to generate a comparison map.

Option SF (Subject genomes FAA files): This option is used for inputting the BLAST search subject genome's FAA file. Where more than one subject genome is used; file names are separated by a coma. (e.g. –QF NC_002179.faa, NC_007514.faa)

Option O (Output type): GCM can generate two varieties of output to display genome comparison maps proving different levels of functionality.

• Option S (Standard): will generate a standalone SVG file to render the genome comparison map.
• Option W (Web based): will generate a thumbnail and a main genome comparison map, both embedded into an HTML page.

VIEW THE EXAMPLE OUTPUT LIVE(Need Adove-SVG plugin Installed - INTERNET EXPLORER ONLY):

• Standalone comparsion map
• web-based comparison map