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.
Paste or upload your sequence(s). The options are described in the Explanation below.
HIValign aligns input sequences to a reference sequences and clips the regions the input touched.
There are five options:
- Always e-mail result
forces your job into background mode.
You will receive an email with a link to the results.
- Align the sequences
chooses the alignment method:
If you uncheck the 'align' option, the input sequences must be pre-aligned.
HMM-align aligns your sequences
based on our curated alignments HMM model.
is a multiple-sequence alignment program that can align large sequences.
MAFFT is faster, but rough. Choose this option if you are interested in aligning untranslated regions.
- Codon-align the sequences
will adjust your alignment so that all codons are intact. A compensating mutation must occur within 5 codons (default)
of an initial frameshift so that the shifted reading frame is left intact.
- Insert a reference sequence
will insert a reference sequence
at the top of your input sequences, before they are aligned and/or clipped.
- Translate to amino acid
will translate your alignment to amino acids. Appropriate symbols are used to represent ambiguous codons.
HIVAlign attempts to automatically recognize the format of your input file by using
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
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.
last modified: Wed Feb 24 14:59 2016