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.
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.
QC/GenBank Tool Explanation
Sequence Quality Control Tutorial
GenBank Entry Generation
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