Do Multiple Sequence Alignment by CLUSTALW and convert the file to a Jbrowse readable WIG file.

This tutorial walks you through how to generate multiple sequence alignment by CLUSTALW and then use the script multialn.pl to convert the output file to a Jbrowse readable wig file.

Note: multialn.pl this script only supports multiple sequence alignments for 3 sequences but can be scaled up very simply by making two changes specified in the script.

Getting Multiple Sequence Alignement Data:

• Go to http://align.genome.jp/
• Set Output Format to CLUSTAL, set Pairwise Alignment to Slow/Accurate, make sure you select DNA as your sequence type.
• Upload a single FASTA file containing all the genomes you wish to compare.
• If you don't understand the additional parameters, leave them alone and click "Execute Multiple Alignment"
• Save the outputted .aln file to your computer.

Convert Clustal output file to WIG using multialn.pl

Run from the terminal with the following parameters:

clustal.aln -> this should be the file you got from running clustal
0 -> this can be 0,1,2 depending on if you are the 1st, 2nd, or 3rd sequence in the FASTA file.
name -> this is the name of your sequence
output.wig -> this is the wig file you are outputting

Sample multialn.pl call:

$ perl multialn.pl clustal.aln 0 NC_004424 output.wig

Add the track to jbrowse from terminal:

/www/jbrowse$ sudo bin/wig-to-json.pl --wig filepath/output.wig --key "Multiple Sequence Alignment"

Then continue to run the generate names script and load your JBrowse in your browser.

• multialn.pl.txt: