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HIV sequence database


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
icon 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
icon Use HIV-1 subtype consensus alignment   subtypes A - K
    include CRF01_AE
icon Select custom background from HIV-1 subtypes and CRFs
icon 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
icon Window size NOTE: window size must be smaller than query!
icon Confidence threshold

icon 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.
icon Score multistate characters as partial matches True   False   (applies to nucleotide queries only)


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
last modified: Thu Jan 21 16:47 2016

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