Sample Analysis

For this example, we show how to align opossum, chicken, and human sequences for the RUNX1 gene. First, prepare the sequences. Go to GenBank and save sequences with the accession numbers AC146773 and AC146486 as plaintext FASTA files. The first one should be saved as "opossum.fasta" (it is the D. virginiana clone used earlier to demonstrate GenomeVISTA) and the second as "chicken.fasta."

To obtain the human sequence, go to the NCBI web site, click on "Map Viewer" in the right-hand column, select "Homo Sapiens" from the drop-down menu, and enter "RUNX1" in the search field. Click on the "Genes Seq" link next to the RUNX1 map element, then on "dl" link in the highlighted line, and then "Display." To save the sequence, click the "Send" button.

Submit the sequences for mVISTA analysis using the procedure described above. Make sure to name the sequences (opossum, chicken, and human), and provide the human annotation. Once you receive an e-mail with a link to the results, view the alignments in VISTA Browser using the human sequence as base. You can now analyze the aligned sequences—look for conserved areas, consider the implications of the differences between the human-chicken and human-opossum alignments, and so on. It is frequently useful to adjust the conservation analysis parameters (see Note 6). Figure 4 shows the results of this mVISTA analysis. The top two rows show what the human-chicken and humanopossum alignments look like when one is using the default parameters. The bottom two rows show the same alignments visualized using a 50-bp calculation window, a 50-bp minimum conserved region width, and an 80% minimum conservation identity.

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