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Mugsy:multiple whole genome alignment tool  

2012-03-07 17:51:01|  分类: 生物信息分析 |  标签: |举报 |字号 订阅

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Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise alignment, a custom graph based segmentation procedure for identifying collinear regions, and the segment-based progressive multiple alignment strategy from Seqan::TCoffee. Mugsy accepts draft genomes in the form of multi-FASTA files and does not require a reference genome.

To cite Mugsy, use:

Angiuoli SV and Salzberg SL. Mugsy: Fast multiple alignment of closely related whole genomes. Bioinformatics 2011 27(3):334-4


Installation
Download mugsy from Sourceforge
cd /path/to/install  tar xvzf mugsy_x86-64-vNrN.tgz  
The release bundle is compiled for x86-64-bit Linux and invoked from a Perl wrapper script. (A pre-compiled version for Mac OSX is not yet available)
Edit mugsyenv.sh and add path to the installation area
export MUGSY_INSTALL=/path/to/install/mugsy  

mugsyenv.sh can then be sourced before invoking mugsy. Alternatively, you can add MUGSY_INSTALL to your environment.
Getting started
Set up the environment
bash  source /path/to/install/mugsyenv.sh  

Run mugsy The input to Mugsy is DNA from two or more genomes in FASTA format. The genomes must be assembled into contigs or scaffolds. For draft genomes, a single multi-FASTA file containing all contigs for the genome should be provided.
mugsy --directory /data/output --prefix mygenomes genome1.fasta genome2.fasta genome3.fasta   

This example will align three genomes and output a file /data/output/mygenomes.maf. The --directory setting is also used for storing temporary files during the run.
The prefix of each input filename will be used as the genome name in the output files (eg. genome1 from genome1.fsa). Header lines in the FASTA files should not contain ':' or '-' to avoid parsing problems.
View or parse MAF output The output of Mugsy is Multiple Alignment Format (MAF).
One option for browsing is
GMAJ, which provides a reference-based stand-alone viewer for MAF files.
java -jar gmaj.jar mygenomes.maf  

Troubleshooting
If the pre-compiled binaries are not compatible with your machine, you may see errors like
ERROR: prenuc returned non-zero, please file a bug report  
To compile Mugsy on your machine, run
svn co https://mugsy.svn.sourceforge.net/svnroot/mugsy/trunk mugsy_trunk  cd mugsy_trunk  make  make install  make dist  

If this succeeds, it will create a file mugsy_x86-64-XXX.tgz containing a fresh set of executables

download:http://mugsy.sourceforge.net/#installation

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