Difference between revisions of "MUMmer"
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MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. For example, MUMmer 3.0 can find all 20-basepair or longer exact matches between a pair of 5-megabase genomes in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop computer. MUMmer can also align incomplete genomes; it can easily handle the 100s or 1000s of contigs from a shotgun sequencing project, and will align them to another set of contigs or a genome using the NUCmer program included with the system. If the species are too divergent for a DNA sequence alignment to detect similarity, then the PROmer program can generate alignments based upon the six-frame translations of both input sequences. | MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. For example, MUMmer 3.0 can find all 20-basepair or longer exact matches between a pair of 5-megabase genomes in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop computer. MUMmer can also align incomplete genomes; it can easily handle the 100s or 1000s of contigs from a shotgun sequencing project, and will align them to another set of contigs or a genome using the NUCmer program included with the system. If the species are too divergent for a DNA sequence alignment to detect similarity, then the PROmer program can generate alignments based upon the six-frame translations of both input sequences. | ||
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==Available versions== | ==Available versions== | ||
* 3.22, 3.23 on RedHat EL6 nodes | * 3.22, 3.23 on RedHat EL6 nodes | ||
Revision as of 02:00, 10 August 2012
Description
MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. For example, MUMmer 3.0 can find all 20-basepair or longer exact matches between a pair of 5-megabase genomes in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop computer. MUMmer can also align incomplete genomes; it can easily handle the 100s or 1000s of contigs from a shotgun sequencing project, and will align them to another set of contigs or a genome using the NUCmer program included with the system. If the species are too divergent for a DNA sequence alignment to detect similarity, then the PROmer program can generate alignments based upon the six-frame translations of both input sequences.
Available versions
- 3.22, 3.23 on RedHat EL6 nodes
Note: mummer requires the perl module to be loaded
Running the application using modules
To use mummer with the environment modules system at HPC the following commands are available:
Get module information for mummer:
$module spider mummer
Load the perl module:
$module load perl
Load the application module:
$module load mummer
or in one command:
$module load perl mummer
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_MUMMER_DIR - directory where mummer is located.
- HPC_MUMMER_BIN - executable directory