LAST

Sequence Aligning Software

Introduction

LAST is a bioinformatics program which is designed to align genomic sequences by finding and aligning similar regions in two ore more different sequence reads. The program is capable of aligning large data sets such as whole vertebrate genomes or very large numbers of DNA sequencing reads. The program has several capabilities such as determining and reporting the ambiguitiy of each column in a given alignment, using available sequence quality information rigorously, aligning DNA sequences to proteins even with frameshifts, comparing PSSMs to sequences and computing the likelihood of randomized sequences being similar by chance.

More information on the package can be found here.

Example

LAST does not require the loading of a module, and is readily available on both Spear and HPC nodes upon login. Using the example from the documentation, first copy some relevant files into an example folder in your home directory,

mkdir ~/last-test
cp /panfs/storage.local/opt/userfiles/last/humanMito.fa ~/last-test
cp /panfs/storage.local/opt/userfiles/last/fuguMito.fa ~/last-test

Working in the test directory, we can align similar regions between the human and fugu mitochondrial genomes.

cd ~/last-test
lastdb -c humdb humanMito.fa

This will generate a number of files which are required in order to compare the fugu genomes to the human genomes,

lastal humdb fuguMito.fa > myalns.maf

Finally to see the results, view myalns.maf in a console-based text editor, or use

less -S myalns.maf