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HIV Sequence Database



Quality Control

HIV-1 Sequence Quality Analysis

Purpose: Examine HIV-1 nucleotide sequences for common problems. Optionally, prepare HIV-1 sequences for submission to GenBank.

Help page | Video tutorial

Input
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Details

Input: The tool accepts HIV-1 nucleotide sequences in Fasta format. Before using, please read the QC/GenBank Tool Explanation.

QC analysis: This tool will perform a set of tests to help you find problems with your sequences. QC results will include:

  • subtype (from RIP),
  • most similar database sequence (from HIV BLAST),
  • phylogenetic tree of each single sequence with subtype references (from Neighbor TreeMaker),
  • phylogenetic tree of all sequences together with subtype references (from Neighbor TreeMaker),
  • number of stop codons and frameshifts (from GeneCutter),
  • hypermutation (from HyperMut).

Understanding your results: The QC/GenBank Tool Explanation gives details about how to assess the results of these analyses. You may also watch our QC tool video tutorial.

Preparing GenBank submissions: This tool can also be used to prepare HIV-1 sequences for GenBank submission. This step is not required. You may choose to only do the QC analysis.

Related Links:
QC/GenBank Tool Explanation
Sequence Quality Control Tutorial (web page)
Sequence Quality Control Tutorial (YouTube video)
GenBank Entry Generation

 

last modified: Tue Jan 23 18:23 2024


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

 
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