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LAST

LAST is a tool which finds similar regions in DNA sequences and aligns them.

LAST is available as a module on Apocrita.

Usage

To run the default version of LAST, simply load the last module:

module load last
$ lastdb -h
Usage: lastdb [options] output-name fasta-sequence-file(s)
Prepare sequences for subsequent alignment with lastal.

Main Options:
-h, --help: show all options and their default settings, and exit
-p: interpret the sequences as proteins
-R: repeat-marking options (default=10)
-c: soft-mask lowercase letters (in reference and query sequences)
-u: seeding scheme (default: YASS for DNA, else exact-match seeds)
[...]

$ lastal -h
Usage: lastal [options] lastdb-name fasta-sequence-file(s)
Find and align similar sequences.

Cosmetic options:
-h, --help: show all options and their default settings, and exit
-V, --version: show version information, and exit
-v: be verbose: write messages about what lastal is doing
-f: output format: TAB, MAF, BlastTab, BlastTab+ (default=MAF)
[...]

A typical session with LAST involves preparing a database with lastdb and then analysing it with lastal, for example:

lastdb -cR01 humdb humanMito.fa
lastal humdb fuguMito.fa > myalns.maf

Core Usage

To ensure that LAST uses the correct number of cores, the -P${NSLOTS} option should be used.

Example jobs

Serial job

Here is an example job running on 4 cores:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 4
#$ -l h_rt=4:0:0
#$ -l h_vmem=2G

module load last
lastdb -P${NSLOTS} -cR01 humdb humanMito.fa
lastal -P${NSLOTS} humdb fuguMito.fa > myalns.maf

When the job completes the output file (myalns.maf) should contain data about the sequence alignments. The tutorial (referenced below) has information about how to interpret the contents of this file.

References