4. Get Genome Alignment Data and Visualization Result

Click button "Structure Analysis" in PGAP-X Lite Launcher, you will get the "Structure Analysis" interface like Figure 4.0.1. Including three functional buttons:

Figure 3.1.1 miss
Figuer 4.0.1: The Three functional buttons in Genome Alignment part.
The Third button "Visualize Genome Alignment Result" will only be available when there is alignment result in your workspace.

4.2. Get Genome Alignment Result In Command Mode

  Click button "Genome Sequence Alignment", you will enter the genome alignment interface like Figure 4.2.1, and Choose "Command Mode".

Figure 4.2.1 miss
Figuer 4.2.1: Genome alignment interface in command mode

  You can enter the Mauve parameters needed, corresponding manual can be found in this link. After entering, click button "Run".

  Wait for seconds, and you can see the aligning process in the buttom part. It may takes you minutes to hours for alignment, depending on the genome number and length.

  When finished, you will get a message like Figure 4.2.2, Click button "Ok", you will get your alignment visualization result directly. At the same time, you can find your alignment result in the folder "GenomeAlignmentResult" in your workspace, and there are two files in the folder,which are "WholeGenomeAlignment.xmfa", and "GenomeName.list". Do NOT try to change its name.

Figure 4.2.2 miss
Figuer 4.2.2: Message in the end of alignment

4.3. Import Your Genome Alignment Result

  Click button "Import Alignment Result of Other Tools", you will enter the import interface like Figure 4.3.1, You should import a genome list file and a alignment result file.

Figure 4.2.1 miss
Figuer 4.3.1: Interface of import
  Genome List file is a list of genome names,which are aligned, the file's format is as follows, it contains two columns, columns one is id, start from 1, and column two is the genome name, column 1 and column 2 are splited by a table-key, or "\t":
1    NC_003028
2    NC_003098
3    NC_008533
4    NC_010380
5    NC_010582
6    NC_011072
  Alignment Result file is alignment result in format of xmfa. Which is a modification of the FASTA multiple alignment format that allows for multiple alignments in a file. Click "Help" button in Lite Launcher to find the detail of this format.

When finished, the button "Import" will be available. Click Import button and file you chosen will be import to your workspace, Pay attention: your former file will be overlaped.