HIV 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

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 is entered

Input Background

Use HIV-1 subtype consensus alignment as background	includes subtypes A - K
Include CRF01_AE consensus
Select custom background from HIV-1 subtype sequences
Use your own alignment as background	NOTE: this set cannot contain more than 26 sequences!
Upload background alignment
Or paste background alignment

Options

Window size	NOTE: window size must be smaller than query!
Confidence threshold
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.
Multistate characters match partially	True False

last modified: Mon Nov 5 11:39 2012

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

Index of all tools	HIV BLAST	Quality Control
ADRA	HIVAlign	QuickAlign
Branchlength	Hypermut	Rainbow Tree
Codon Alignment	jpHMM at GOBICS	Recombinant HIV-1 Drawing Tool
Consensus Maker	Mosaic Vaccine Tool Suite	RIP
ELF	Motif Scan	SeqPublish
ElimDupes	N-Glycosite	Sequence Locator
Entropy	PCOORD	SNAP
FindModel	PepMap	SUDI Subtyping
Format Converter	PeptGen	SynchAlign
Gap Strip/Squeeze	PhyloPlace	Translate
GenBank Entry Generation	PhyML	TreeMaker
Gene Cutter	Pixel	TreeRate
Heatmap	Poisson-Fitter	VESPA
Hepitope	Protein Feature Accent	External Tools
Highlighter	Protein Structure