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Old 03-31-2012, 10:58 AM   #1
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Location: UK

Join Date: Mar 2012
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Default Alignment of >30 genomes with mauve?

Hi all,

Relatively new to all this, I tried progressiveMauve to align more than >25 bacterial genomes and it repeatedly crashed after a few hours. When I align ~10 it works perfectly. I was told by other members of my lab that mauve tends to not work so much with a larger number of genomes.

The question may seem trivial to most of you, sorry in advance, but which genome alignment tool would you use to do this? Still, I like mauve; so would there be a way for it to work with a larger number of genomes?

Thanks for your time and help!


gmer is offline   Reply With Quote
Old 03-31-2012, 11:33 AM   #2
Location: Washington DC

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Default Whole Bacterial Genome Alignment

Of course, Mummer is the classic 'alignment' tool; and Progressive Mauve is built to purpose; but I may have something which can help you - a colleague has built a tool that uses progressive ortholog identification to construct phylogenies; but by virtue of the method, it can provide the core information for a progressive alignment as well - and currently it is robust to a relatively large number of genomes. It would need some extension to provide assembled whole genome or contig alignment.
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Old 03-31-2012, 11:52 AM   #3
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I've successfully aligned 20 genomes with Mauve but it took some time, over a day and I needed to assign extra memory to the task (do this via the Java options a la

You might also want to consider looking at Mugsy from the Salzberg group (http://bioinformatics.oxfordjournals...tq665.abstract) which can apparently align 31 Streptococcus genomes in 2 hours.

And of course bckirkup's suggestion sounds interesting too!
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Old 04-01-2012, 07:01 AM   #4
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I will try Mugsy and come back here if any other problem. Thanks!

@bckirkup: what's the name of the tool made by your colleague?

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Old 04-07-2012, 08:57 PM   #5
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Location: New Jersey

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Default Reg Mugsy Usage


I am trying to align human chr1 and mouse chr 1 using Mugsy. I am facing difficulties in getting it to work.

These are the steps I followed. Can someone help.

I have the 2 files Ch1_human, chr1_mouse in FASTA format.

I could install Mugsy
It asks me to set the the MUGSY_INSTALL path. I set it using
export MUGSY_INSTALL= <working directory>

source <path of>

I dont have root permissions on the server I use.

I get the following error in mugsy.
20120407|225222| 4601| ERROR: The following critical files could not be used
20120407|225222| 4601| ./mugsy_output/
20120407|225222| 4601| ./mugsy_output/tmp.chr1.cluster
20120407|225222| 4601| ./mugsy_output/tmp.chr1.mgaps
20120407|225222| 4601| ./mugsy_output/tmp.chr1.ntref
20120407|225222| 4601| /afs/
20120407|225222| 4601| /afs/
20120407|225222| 4601| Check your paths and file permissions and try again

I checked the file permissions. it is proper.

can anyone please help ?
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