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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
Organism
Region

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:

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:

last modified: Thu Dec 22 13:01 2011


Questions or comments? Contact us at seq-info@lanl.gov.

 
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