HIV sequence database

RIP

Recombinant Identification Program

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.

` For bulk uploads, just paste or upload all sequences. An e-mail address is required in order to send results back.

Input Query

Upload your query sequence file
Or paste your query sequence(s) [Sample Input]
Or enter a GenBank accession number
E-mail address (only required for bulk upload)

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	NOTE: this set cannot contain more than 20 sequences!
Upload your alignment here
Or paste your alignment here

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: Fri Oct 21 13:00 2011

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

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