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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 or upload your sequence(s). The options are described in the Explanation below.

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 acids
(DNA seqs only)

Note: This program is computationally intensive and may take some time to complete.
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 genes that 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 computationally intensive. An input file that is pre-aligned and smaller than 500 Kb will run immediately (no e-mail, unless you chose the option to always e-mail the result). If your input file exceeds the limit, or if your sequences required aligning, your job will be run in batch, and you will receive an e-mail with a link to your results.

References:

last modified: Wed Feb 24 14:59 2016


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

 
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