Recombinant Identification Program: RIP 3.0

Purpose: RIP helps identify recombination in a query sequence by calculating its similarity to a background alignment of HIV-1 sequences of different subtypes in a sliding window.

Usage: Each RIP job requires two inputs from the user, a query sequence, and a background alignment. The total number of sequences is limited to 50. There are 3 options for providing the background alignment.

• The HIV database standard HIV-1 subtype consensus alignment is the RIP 3.0 default background. Under this option RIP aligns your query to this background automatically. The resulting alignment can be downloaded.
• You can construct a custom background from a list of representative subtype sequences we provide. Your query will be automatically aligned to this custom background.
• You supply the background. In this case the background must already be aligned to your query sequence, and in the same format. The background alignment must not contain the query sequence. Most standard formats are automatically recognized.

Window size and significance threshold are adjustable. Alignment gaps may be treated in four different ways. Multistate character codes (IUPAC) in your alignment can be scored as partial matches or as mismatches. When your analysis is complete you can create an illustration of the recombinant genome with our Recombinant HIV-1 Drawing Tool.

For additional details, see RIP Explanation.