HIV Databases HIV Databases home HIV Databases home
HIV sequence database



GenSig

Purpose: identify genetic signatures in a DNA alignment with associated phenotypic data. See explanation.

Analysis type
Strategy icon Full phylogenetic and signature analysis
New signature analysis using phylogenetic analysis from a previous run
Sequence alignment and options
Codon-aligned DNA sequences
[Sample Input]

Ambiguity codes icon Replace with 'N'   No ambiguity codes in sequences
Non allowable chars in names ( ; : ( ) , # | . - ) icon Replace with '_'   No such characters in names
HIV-1 and HXB2 icon This is a HIV-1 alignment and the 1st seq is HXB2    Not HIV-1 or HXB2 not included
  Regions of interest
Phenotype data and options
Phenotype data icon
Delimiter Comma   Space   Tab
Mismatched names icon Ignore mismatched sequence names between alignment and phenotype data
Statistical test icon Fisher's test. No optimization need. Values are 1, 0, or -1.
Fisher's test. Set highest decile to 1
Fisher's test. Set highest quartile to 1
Fisher's test. Set above median to 1
Fisher's test. Set highest three quartiles to 1
Fisher's test. Set highest nine deciles to 1
Wilcoxon test. Values are continuous.
Signature options
Signature analysis icon
sD1: Single site with depth of 1
sD2: Single site with depth of 2
sD3: Single site with depth of 3
glyco: Glycosylation analysis
Maximum q-value icon


Reference:

Related links:

last modified: Wed Jan 16 08:49 2019


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

 
Operated by Triad National Security, LLC for the U.S. Department of Energy's National Nuclear Security Administration
© Copyright Triad National Security, LLC. All Rights Reserved | Disclaimer/Privacy

Dept of Health & Human Services Los Alamos National Institutes of Health