HIVAlign

VirAlign for HIV sequences

Purpose: HIValign takes aligned or unaligned sequences and gives the alignment of the region which the input sequences touched. If your sequences aren't pre-aligned, this tool can align them via a Hidden Markov Model or MAFFT.

Usage: Paste your sequence(s) into the space provided, or browse for your file. Then you may choose options.

Explanation: Please read the Explanation below before using.

Input

Paste your sequence(s) [Sample Input]
Or upload your sequence file
DNA/Protein	DNA Protein
Organism	HIV-1/SIVcpz HIV-2/Other SIV Let program decide
Region	Complete Gag Pol Vif Vpr Tat Rev Vpu Env Nef

Options

Always e-mail result
Align the sequences	By HMM-align     By MAFFT
Codon-Align the sequences (DNA seqs only)	Allow codons to compensate frameshift
Insert a reference sequence	HXB2 for HIV-1, or SIVMM239 for HIV-2 and SIV
Translate to amino acid (DNA seqs only)

Note: This program is computationally intensive and may take a while to run. Please don't resubmit your request!

Explanation: HIValign aligns input sequences to a reference sequences and clips the regions the input touched. There are five options:

• The first option forces your job into background mode. You will receive an email with a link to the results.
• The second option asks the program to align your input sequences in one of two ways:
  • HMM-align aligns your sequences based on our curated alignments HMM model.
  • MAFFT is a multiple-sequence alignment program that can align large sequences. MAFFT is fast, but rough.
  If you have not checked the 'align' option, the input sequences must be pre-aligned.
• The third option codon-aligns your sequences based on the reference sequence. A compensating mutation must occur within 5 codons (default) of an initial frameshift so that the shifted reading frame is left intact.
• The fourth option inserts a reference sequence at the top of your input sequences, before they are aligned and/or clipped.
• The fifth option translates your alignment to protein sequence.

HIValign attempts to automatically recognize the format of your input file by using Format Converter. The results page summarizes the running parameters and information about the input, and gives you the alignment of the region which the input touched or you selected . From this page you can download the alignment in different formats, or send the resulting alignment to TreeMaker or FindModel.

Aligning large sequences is a computationally intensive procedure. An input file that is pre-aligned and smaller than 500 Kb is run immediately. If your input file exceeds the limit, or if you checked the 'Align' option , or let program decide the model , your job will be run in batch, and you will receive an email when it has finished. The email contains link to your results.

References:

• HMMER website
• MAFFT (Multiple sequence alignment)
• Eddy SR. Profile hidden Markov models. Bioinformatics 1998.14(9):755-63.
• Gaschen B, Kuiken C, Korber B, Foley B. Retrieval and on-the-fly alignment of sequence fragments from the HIV database. Bioinformatics 2001.17(5):415-8