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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