An example Fasta file can be found in:
[Install directory]\Example\HIV ENV DNA.fasta
To get familiar with CAUSA, you may analyze the example as followed:
Step 1: Click the load menu/tool, Load the sample fasta file: HIV ENV DNA.fasta, which contains 17 coding DNA sequence for HIV envelop protein (ENV).
When the cDNA/mRNA Sequence files (*.fasta) is loaded, they were displayed as in Figure 3-1. In which every 64 different triplet codons are colored with a different color, makes the sequences looks like a rainbow!
Figure 3-1. CAUSA: the rainbow-like sequence displayer
Step 2: Click Align Menu/tool. You will see a popup window shown as Figure 3-2, in which the CLUSTALW program is executed. This process may take a few minutes, depending on how many sequences are loaded.
Notice: In the sequence names (following “>” in the fasta file), space and non-alphanumeric characters are not recognizable by ClustalW. So CAUSA will remove any spaces and non-alphanumeric characters in the sequence names to prevent errors from occurring.
Figure 3-2 ClustalW alignment in process
When the ClustalW window finished and closed, the unified alignment is displayed in three views, as shown in Figure 3-3.
Figure3-3 CAUSA: combined alignment views
Step 3: Click the export menu/tool, input path and filename, then click the export button, the result will be saved in three .fasta files, and the directory will be displayed.
Figure 3-4. Export the combined alignment to a DNA alignment and a protein alignment
This is the output of CAUSA. You may use the DNA or the protein sequence alignment for molecular phylogeny trees construction, or the protein sequence alignment for homology structure modeling.