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This kit will include gcc, ar, and make which are necessary for building MUMmer. Compilation and installation For explanation purposes, let's suppose you just downloaded the MUMmer3.

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Running nucmer Like mummer, nucmer can handle multiple reference and query sequences, however this example will demonstrate the alignment of multiple query sequences to a single reference. We will align a number of B.

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After which, the matches are clustered and the matches within clusters are extended via Smith-Waterman techniques in order to expand the total alignment coverage and close the gaps between clustered MUMs. The "out. In addition, dotplots can be generated if you have gnuplot installed via the 'mummerplot' script.

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For multiple switches, order of operations is as follows: -i -l -u -q -r -g -m -1 -b. If an alignment is excluded by a preceding operation, it will be ignored by the succeeding operations. An important distinction between the -g option and the -1 and -m options is that -g requires the alignments to be mutually consistent in their order, while the -1 and -m options are not required to be mutually consistent and therefore tolerate translocations, inversions, etc. In general cases, the -m option is the best choice, however -1 can be handy for applications such as SNP finding which require a 1-to-1 mapping.

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