Bioinformatics Mutation, Recombination, and Single Nucleotide Polymorphism

Analytical and Computational Tools

• HIV Database
  
  • Hypermut/Analysis and Detection of APOBEC-induced Hypermutation
    Documents the nature and context of nucleotide substitutions in a sequence population relative to a reference sequence.
  • RIP/Recombinant Identification Program
    Identifies recombination in query sequence(s) by calculating similarity to a background alignment in a sliding window.
• Immunology Database and Analysis Portal (ImmPORT)
  
  • Haploview
  • Tag SNP
• Influenza Research Database (IRD)
  
  • Identify Point Mutations
    This tool will scan the specified proteins that are from type A viruses with the specified subtype found in the IRD database for the presence of the amino acid you specify at the coordinate (location) indicated.
  • Analyze Sequence Variation (SNP)
    Sequences are grouped by segment number, flu type, subtype, and host and are aligned.

Databases and Data Sets

• Database of Mutations Causing Human Hyper Ige Syndrome (STAT3base)
• EuPathDB Search
• HIV Databases
  
  • ADRA/Antiviral Drug Resistance Analysis Tool
    ADRA can be used to help researchers rapidly find studies related to a mutation of interest.
  • HIV-1 Resistance Mutation Database
• Influenza Research Database Sequence Feature Variant Types
  Provides data on specific characteristic regions and/or sub-regions termed "Sequence Features" defined for all influenza virus proteins.
• SNP Query

Visualization and Modeling Tools

• ImmPORT/GBrowse Genome Browser
• Recombinant HIV-1 Drawing Tool
  This tool maps recombinant breakpoint data for HIV-1 onto a map of the HXB2 genome.
• Single Nucleotide Polymorphism (SNP) Explorer
  Analysis and visualization of hyper-igm/cvid re-sequencing microarray data.

Contact Information

For more information on Bioinformatics Mutation, Recombination, and Single Nucleotide Polymorphism, email:
Bioinformatics and Computational Sciences Branch

Content last reviewed on January 24, 2013