Manual

GenomePlot (Genome Comparison Diagonal Plot)

1. Introduction

GenomePlot (Genome Comparison Diagonal Plot Generating Tool) is a group of CGI programs to generate genome comparison diagonal plot and its image map. GenomePlot is currently embedded in the PLATCOM system and uses pre-computed all pairwise comparison database (PCDB).

Currently ~ 150 complete genomes are provided in the list, but, unfortunately, some genomes are incomplete and need to be updated in the near future. If you cannot get the expected result, this might be the one of the reason. GenomePlot is an easy plot generating tool and generates 2 types of plot : (1) Protein-protein pairwise comparison plot and (2) Whole genome-genome(DNA) pairwise comparison plot (see Fig. 3). DNA-DNA GenomePlot is not provided temporarily.

Even though this is a simple program, it provides users a strong intuition to understand the genome structure and phylogenetical distance between given 2 genomes when it is used with PLATCOM's OperonViz tool.

2. How to Use

You may choose GenomePlot service from PLATCOM web site. GenomePlot service request form is as follows. A user can may choose 2 or more genomes from the genome list.

Fig 1. GenomePlot Web Interface

5 parameters should be submitted via service request form : For Protein-Protein Plot, (1) Protein Length, (2) Z-score, (3) E-value and For DNA-DNA Plot, (1) DNA sequence, (2) length, (3) Percent Identity (PIP). Because GenomePlot generates 2-D plot, only 2 genomes should be selected from the genome list by marking box. DNA-DNA GenomePlot is not provided temporarily.

Fig 2. Submission Result

When all parameters and genomes (e.g. A, B, and C) are submitted, GenomePlot automatically generates all possible 2D plots (A-B, A-C, and B-C) and their image maps. These image maps can be seen in a new window by clicking the provided links.

Fig 3. Buttons, Sliding Bars, Plot Information

Now you have a plot. Blue dots stand for sequence matches (homologs) satisfying given cutoff values. Zoom-in/out buttons, sliding bars (8 directions) and information windows are provided. You can zoom-in or -out by simply clicking using buttons or by typing ranges in the windows provided below a plot.

Altenatively, you may use k/K for 1000 and m/M for 1,00,000. That is, 2.1m can be used instead of 2100000.

Fig 4. Further Analyses

When you click any blue dot in the plot, it will generate a page to provide protein sequences and more analysis tools for further investigation. NCBI's EntRez protien information (Fig 5) and CDD(NCBI's Conserved Domain Database, Fig 6) are currently provided. The latter is very useful when you are interested in finding a common motif between these 2 proteins.

Fig 5. NCBI EntRez Protein Information

Fig 6. NCBI CDD

If you want to run FASTA for these 2 proteins, just click a provided link to run it.

Fig 7. FASTA Result