MUMmer can also align incomplete genomes; it handles the 100s or 1000s of contigs from a shotgun sequencing project with ease, and will align them to another set of contigs or a genome, using the NUCmer utility included with the system. The PROmer utility takes this a step further by generating alignments based upon the six-frame translations of both input sequences. PROmer permits the alignment of genomes for which the proteins are similar but the DNA sequence is too divergent to detect similarity.
Any publications using MUMmer should cite the papers listed on MUMmer homepage .
Version
The screen output of MUMmer includes the version number.Running MUMmer on Helix
MUMmer v 3.2 on Helix is installed in /usr/local/mummer. To use it, you need to add the MUMmer directories to your path, as in the sample session below. If you expect to use MUMmer frequently, you should add the PATH commands to your .cshrc or .bash_profile file to avoid typing them in each session.helix% export PATH=/usr/local/mummer:$PATH (for bash shell users) helix% setenv PATH /usr/local/mummer:$PATH (for csh or tcsh users)
Sample session (user input in bold): This session uses the input files at The Mummer website
<helix>% ls D_melanogaster_2Rslice.cds D_melanogaster_2Rslice.utr H_pylori26695_Eslice.fasta D_melanogaster_2Rslice.fasta D_pseudoobscura_contigs.fasta H_pyloriJ99_Eslice.fasta <helix>% setenv PATH /usr/local/mummer:$PATH <helix>% promer -p promer D_melanogaster_2Rslice.fasta D_pseudoobscura_contigs.fasta 1: PREPARING DATA 2,3: RUNNING mummer AND CREATING CLUSTERS # reading input file "promer.aaref" of length 71202 # construct suffix tree for sequence of length 71202 # (maximum input length is 536870908) # CONSTRUCTIONTIME /usr/local/MUMmer3.20/mummer promer.aaref 0.02 # reading input file "promer.aaqry" of length 84243 # matching query-file "promer.aaqry" # against subject-file "promer.aaref" # COMPLETETIME /usr/local/MUMmer3.20/mummer promer.aaref 0.04 # SPACE /usr/local/MUMmer3.20/mummer promer.aaref 0.15 4: FINISHING DATA <helix>% show-coords -r -c -l -L 100 -I 50 promer.delta > promer.coords <helix>% show-aligns promer.delta "D_melanogaster_2Rslice" "3214968" > promer.aligns <helix>% mapview -n 1 -p mapview promer.coords <helix>% mummer -mum -b -c H_pylori26695_Eslice.fasta H_pyloriJ99_Eslice.fasta > mummer.mums # reading input file "H_pylori26695_Eslice.fasta" of length 275287 # construct suffix tree for sequence of length 275287 # (maximum input length is 536870908) # process 2752 characters per dot #.................................................................................................... # CONSTRUCTIONTIME mummer H_pylori26695_Eslice.fasta 0.10 # reading input file "H_pyloriJ99_Eslice.fasta" of length 265111 # matching query-file "H_pyloriJ99_Eslice.fasta" # against subject-file "H_pylori26695_Eslice.fasta" # COMPLETETIME mummer H_pylori26695_Eslice.fasta 0.34 # SPACE mummer H_pylori26695_Eslice.fasta 0.52 <helix>% mummerplot -x "[0,275287]" -y "[0,265111]" -postscript -p mummer mummer.mums gnuplot 4.0 patchlevel 0 Reading mummer file mummer.mums (use mummer -c) Writing plot files mummer.fplot, mummer.rplot Writing gnuplot script mummer.gp Rendering plot mummer.ps
