QuickAlign

	Conventional		Discontinuous

Purpose: Use coordinate positions to obtain desired region(s) from our premade alignments, or from your own alignment. Multiple regions are concatenated into a single alignment. Details and help files below.

Alignment

Alignment

LANL database alignment   user alignment

LANL alignment options

Alignment type	Filtered web  Web  Subtype reference  Compendium
Organism	HIV-1/SIVcpz  HIV-2/SIVsmm   Other SIV
Region	Complete 5'LTR Gag Pol Vif Vpr Tat Rev Vpu Vpx Env Nef
Sequence type	nucleotide   amino acid
Positions of interest (Residues of ref seq) [Sample Input]

User alignment options

Paste alignment
Or upload
Organism	HIV-1/SIVcpz  HIV-2/SIVsmm   Other SIV   Other
Reference sequence	included (must be the 1st sequence in the alignment; only for HIV-1, HIV-2, SIV)
Positions of interest
Position numbers refer to	residues of 1st sequence alignment columns, including gaps
Summarize results by	first character(s) in names the characters in field of names delimited by paste or upload grouped sequence names (example)

Options

Display wide output	yes no
Calculate frequency by position and show logos	cut-off %
Remove residues from logos	consensus of alignment consensus of seq group residues of 1st seq of alignment residues of 1st seq of seq group show all
Mark potential N-linked glycosylation sites	yes no      (for proteins only)

Details

• QuickAlign Explanation explains the tool and its options.
• QuickAlign Results explains how to interpret your results.

Related links:

• Alignments describes the different types of premade alignments available.
• Gene Map provides sequence coordinates for the genes and regions of HIV-1.
• Reference Sequence Search provides sequence coordinates for features of HXB2 (HIV-1) and Mac239 (HIV-2/SIV).
• Sequence Locator provides more detailed location information, but does not produce an alignment to database sequences.