HCValign
Purpose: HCValign takes one or more nucleotide sequences in any standard format and
aligns them to our
curated alignments
via the appropriate Hidden Markov Model,
or aligns them using multiple sequence alignment by the multiple alignment program
MAFFT.
Usage:
Paste your sequence(s) into the space provided, or browse for your file.
Then, you may choose options
.
Explanation: below
Note: This program is computationally intensive and may take a while to run. Please don't resubmit your request!
Explanation:
HCValign was developed mainly from a implementation of
HMMER package.
There are five options:
-
Check the first option to force your job into background mode;
you will receive an email with a result link when the program has finished.
-
Check the second option to have the program align your input sequences, in one of two ways:
-
hmm-align aligns your sequences
based on our curated DNA alignments HMM model.
-
MAFFT
is a multiple-sequence alignment program which can align large sequences.
MAFFT is fast, but rough.
If you have not checked the 'align' option, the input sequences must be pre-aligned.
-
Check the third option to have the program codon align your sequences
based on the reference sequence. A compensating mutation is within 5 codons (default)
of an initial frameshift so that the shifted reading frame is left intact.
-
Check the forth option to have the reference sequence inserted
at the top of your input sequences, before they are aligned.
-
Check the final option to have your alignment translated to protein sequence.
HCValign attempts to automatically recognize the format of your input file by using
Format Conversion.
The result page summarizes the running parameters and information about input, and gives you
the alignment of the region which the input touched
, and allows you to download the alignment in different formats, and uses result alignment to do
TreeMaker or
FindModel program.
Aligning large size sequences is a computationally intensive procedure.
Currently, input file which is pre-aligned and smaller than 500 Kb for the user
selected model is run immediately; if your input file exceeds the limit, or checks 'Align' option
, 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:
Questions or comments? Contact us at
hcv-info@lanl.gov