Manual for GAME (Genome Alignment by Match Extension)

1. Introduction

GAME (Genome Alignment by Match Extension) is a program to align genomic DNA sequences. User can use their own sequences or select 200 complete genomes in a list. The generated alignments are shown in web browser and can be downloaded to the client. The overall structure and biological events, such as recombination, between two genomes are visualized by gamev applet.

2. How to Use

To request GAME web service,
(1) set parameters or use the default values (Fig. 1a),
(2) upload genomic DNA sequences or choose two genomes from genome list (Fig. 1b).

(a)	(b)
Fig 1. GAME Web Interface

GAME web service generates the results as shown in Fig. 2.
First, it shows the information for uploaded or chosen sequences and parameters. Clicking Download link downloads the result of alignments, and Clicking Visualization link runs the visualization applet. Then the alignment results are summarized and each alignment shows by clicking alignment number link (Fig. 3).

Fig 2. GAME Output

Fig.3 shows the information of an alignment. The first line shows number, starting position in the first genome, starting position in the second genome, lenth in the first genome, lenth in the second genome, strand of the second genome, and score. Clicking ↑ goes to the previous alignment result, clicking ↓ goes to the previous alignment result, and clicking NCBI shows the annotation around alignment region (Fig. 4).

Fig 3. Alignment View

Fig 4. The Annotation around alignment region on NCBI

Game web service provides a visualization applet for genome alignments. It supports Various functions such as zooming, filtering, and information.

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Fig 5. GAME Visualization Applet