HIV sequence database

Recombinant Identification Program: RIP 3.0

Purpose: RIP identifies recombination in a query sequence by calculating its similarity to a background alignment of HIV-1 sequences of different subtypes in a sliding window. For details, see RIP Explanation.

Input Query

Upload your query sequence file
Or paste your query sequence [Sample Input]
Or enter a GenBank accession number

Input Background

Use HIV database subtype consensus alignment as background
Include CRF01_AE consensus
Select custom background from subtype consensuses
Use your own alignment as background
Upload your alignment here
Or paste your alignment here

Options

Window size
Significance 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: Tue Jun 30 15:30 2009

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

Index of all tools	ADRA	Branchlength
Codon Alignment	Consensus Maker	ELF
ElimDupes	Entropy	Epilign
FindModel	Format converter	Gap strip/squeeze
Gene Cutter	HDent/HDdist	Heatmap
Hepitope	Highlighter	HIV BLAST
HIValign	Hypermutation	jpHMM at GOBICS
Mosaic Vaccine Tool Suite	Motif Scan	N-Glycosite
ODprep/ODfit	PCOORD	PepMap
PeptGen	PhyloPlace	PhyML
Pixel	Primalign	Protein Feature Accent
Protein structure	Quick Align	Recombinant HIV-1 drawing tool
RIP	SeqPublish	Sequence locator
SNAP	SUDI subtyping	SynchAlign
Translate	Treemaker	TreeRate
VESPA	External tools