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Recombinant HIV-1 Drawing Tool Explanation

Details

Sample Input
Your data should look like the sample data below. Separate data with a space or tab.

1 2677 G
2678 3345 A
3346 3423 A/J
3424 5123 J
6000 6899 ?
6900 7144 A
7145 9719 G

Sample Output
The output you would get from the data above is shown here. The actual drawing you obtain will be larger than the one shown below, allowing you to adjust the image as needed for display or publication.

Genome map image

Input requirements
If you submit the data as a file, it can be either a text file or an Excel spreadsheet (be sure to check box). If using a text file, it should have spaces or tabs between each column and a carriage return at the end of each row.

The first column lists the start of each subtype region, the second column the end of that region, and the third column the subtype of that region. Each row describes the next region in the genome. In this example, there is a precise breakpoint between subtypes G and A at positions 2677 - 2678. If the breakpoint position is imprecisely known, but is known to occur in a certain span, indicate this as shown in row 3 of the table above. The given subtype ("A/J") indicates that the breakpoint between the A region and the downstream J region is uncertain, but that the breakpoint occurs in this span. In the illustration, such uncertain breakpoint regions are illustrated by an interfingering of the two colors, and the breakpoint in such regions is shown at the center and expresses the size of the regions using a plus or minus notation. Don't confuse this concept of uncertain breakpoint with a region of uncertain or unknown subtype. The latter is indicated by "?" or "U" (row 5) and means that that region cannot be assigned to a known subtype. Note also that the region between 5124 and 5999 is absent in the table above, and appears uncolored in the illustration. This means no information is available, probably because that span was not sequenced.

If possible, breakpoints should be expressed in HXB2 coordinates; in this case, leave the bottom two input boxes empty. If your breakpoint data are in the coordinates of your sequence, you can automatically convert them to HXB2 coordinates by checking the "Non-HXB2" box and pasting in or uploading your sequence.


last modified: Tue Dec 17 11:10 2013


Questions or comments? Contact us at seq-info@lanl.gov.

 
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