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HIV sequence database

QuickAlign v1

NOTE: This version of QuickAlign is no longer maintained. For additional features and options, please visit QuickAlign v2.

Purpose: Align a desired region to our premade alignments or your own alignment. Details and help files below.

Provide query sequence(s)
Paste your sequence(s) here
or upload sequence file
-- OR leave both fields above blank, and --
Choose region coordinates
Sequence coordinates start end
(HXB2 coordinates for HIV-1; Mac239 coordinates for HIV-2 or SIV)

Organism HIV-1 HIV-2 SIV other
Query sequence type nucleotide protein let program decide
Alignment Use LANL database alignment
Use user alignment
Delete gaps and shift alignment to C-terminus yes no      (for proteins only)
Display wide output yes no
Calculate frequency by position      cut-off %
Include surrounding region


QuickAlign was formerly offered as the Primalign and Epilign tools.


Related links:

  • Alignments describes the different types of premade alignments available.
  • The Gene Map page provides sequence coordinates for the genes and regions of HIV.
  • Sequence Locator provides additional location information, but does not produce an alignment to database sequences.
last modified: Wed Sep 17 11:08 2014

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