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HFV Ebola sequence database
 

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
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
     
icon Customize background from HIV-1 subtypes and CRFs
icon Use your own alignment as background
     
     
     
Options
icon Window size NOTE: window size must be smaller than query!
icon Confidence threshold

icon Gap handling


icon Score multistate characters as partial matches     (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



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