RIP

Recombinant Identification Program

Purpose: RIP identifies recombination in query sequence(s) by calculating similarity to a background alignment in a sliding window. For details, see RIP Explanation.

Input Query

Upload your query sequence(s)
Or paste your query sequence(s) [Sample Input]
Or enter a GenBank accession
E-mail address	(required if >1 sequence entered)

Input Background

Use HIV-1 subtype consensus alignment	subtypes A - K
	include CRF01_AE
Select custom background from HIV-1 subtypes and CRFs
Use your own alignment as background	maximum 26 sequences
Align your query and custom background	Check box if custom background is not aligned with query.
Upload background alignment
Or paste background alignment

Options

Window size	25 50 100 200 300 400 500 600 800 1000 NOTE: window size must be smaller than query!
Confidence threshold	none 90% 95% 99%
Gap handling	Treat gaps as characters; Plot all window values. Treat gaps as characters; Don't plot window values for gaps. Strip all gaps; Plot all window values. Strip all gaps; Plot blanks where gaps used to be.
Score multistate characters as partial matches	True   False   (applies to nucleotide queries only)

Reference

A computer program designed to screen rapidly for HIV type 1 intersubtype recombinant sequences.
Siepel AC, Halpern AL, Macken C, Korber BT.
AIDS Res Hum Retroviruses. 1995 Nov;11(11):1413-6.
Link to: PubMed or text online