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.
The minimum cluster size here is bumped up to -c The two output files are prefixed by the string specified with the -p option. At this stage, the alignment of the two inputs is complete, however it is necessary to parse the nucmer.
Running show-coords To view a summary of all the alignments produced by NUCmer, we can run the nucmer. Each line of the table represents an individual pairwise alignment, and each line is sorted by its starting reference coordinate -r.
Additional information, like alignment coverage -c and sequence length -l can be added to the table with the appropriate options.
Output is to stdout, so we have redirected it into the file, nucmer. Running show-snps To view a summary of all the SNPs and indels between the two sequence sets, we need to run the nucmer. Each line of the table represents a single mismatch in the pairwise alignment.
This kit will include gcc, ar, and make which are necessary for building MUMmer.
With the -C option, only SNPs from uniquely aligned regions will be reported. Additional information can be added or removed with the command line switches described in the manual.
Running show-tiling To produce a minimal tiling of contigs across the reference sequence, we need to run the nucmer. This output can aid the closure of a draft genome when a closely related organism has already be finished. Viewing the output nucmer and show-tiling output can both be viewed with mummerplot, however these plots alignment delta options offer little more information in regards to this example.
It follows the exact same steps as NUCmer and even uses most of the same programs in its pipeline, with one exception - all matching and alignment routines are performed on the six frame amino acid translation of the DNA input sequence.
This provides promer with a much higher sensitivity than nucmer because protein sequences tends to diverge much slower than their underlying DNA sequence. Therefore, on the same input sequences, promer may find alignment delta options conserved regions that nucmer will not, simply because the DNA sequence is not as highly conserved as the amino acid translation.
- software recommendation - visualisation of genome alignment - Bioinformatics Stack Exchange
- The MUMmer 3 manual
Alignment delta options the following sections, a short example is given that demonstrates how to use promer. This example aligns a few query sequences to single reference sequence using promer; displays alignment delta options alignment coordinates using show-coords; and prints a pairwise alignment of one of the contigs using show-aligns.
The following input files will be used to demonstrate this example:.