HIValign

This is a beta version! There may be bugs or other problems. Please use with GREAT care and let use know any problems you have. Since this tool is being actively developed, we will fix them quickly.

Purpose: HIValign takes one or more nucleotide sequences in any standard format and aligns them to our sequence Hidden Markov Model, or does multiple sequence alignment by the multiple alignment program. This tool can be used to align your sequences based on our curated DNA alignments.

Usage: Paste your sequence(s) into the space provided, or browse for your file. Then, select a HMM Model and a region.

Explanation: HIValign was developed mainly from a implementation of HMMER package. There are four options can be chosen. Frist option would force your job into background mode and you can receive an email with result link when program has finished. Second, there are two ways to align your input sequences. Hmm-align is the alignment based on our curated DNA alignments HMM model. MAFFT is a multiple sequences alignment program which can align large sequences fast but rough. Third option decides whether or not to codon align sequences based on the reference sequence. The fianl option is to insert the reference sequence in the top of your input. HIValign 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 you selected or the touched regions when you select "Complete", and allows you to download the alignment in different formats, and uses result alignment to do TreeMaker and FindModel program.

Aligning large size sequences is a computationally intensive procedure. Currently, input files which is pre-aligned smaller than 500 Kb or which is not pre-aligned smller than 50 Kb for the user selected model are run immediately; if your input file exceeds the limit or uses the model by program decide, your job will be run in batch, and you will receive an email when it has finished. The email contains link to your results.