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Quality Control

HIV-1 Sequence Quality Analysis

Purpose: (1) Examines sets of HIV-1 nucleotide sequences for common problems. (2) Prepares HIV-1 sequence sets, together with related data, for submission to GenBank.

Input: The tool accepts HIV-1 nucleotide sequences in Fasta format. Before using, please read the QC/GenBank Tool Explanation. If you have already performed QC analyses and you only want to generate a Sequin file, you can also use the GenBank Entry Generation tool.

Input
Paste your sequence set
Upload your sequence set
Enter a job title
Enter your e-mail address

 


Details

QC analysis: This tool will perform a set of tests to help you find problems with your sequences. The QC/GenBank Tool Explanation gives details about how to assess the results of these analyses. 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).

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

Related Links:
QC/GenBank Tool Explanation
Sequence Quality Control Tutorial
GenBank Entry Generation

 

last modified: Wed Feb 23 12:01 2011


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

 
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