Run Mapview (MUMmer) online to display sequence alignments from MUMmer, NUCmer, PROmer or Mgaps. MUMmer , NUCmer, and PROmer are described in "Fast Algorithms for .. See top of script for more information, or see if mummerplot or mapview has the. MuMmer package example. To run MuMmer at the command line: scc4% module load mummer/ scc4% mapview -n 1 -p mapview
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The 5' and 3' UTRs are colored pink and blue to indicate the gene's direction of translation.
- InsideDNA: mapview - Display sequence alignments from MUMmer, NUCmer, PROmer or Mgaps
- Mapview(1) — mummer — Debian testing — Debian Manpages
- The MUMmer 3 manual
- Mapview description
PROmer matches are shown twice, once just below the reference genome, where all matches are collapsed mummer mapview red boxes, mummer mapview in a larger display showing the separate matches within each contig, where the contigs are colored differently to indicate contig boundaries.
Percent identity is of the amino acid translations used by PROmer.
Matches from the same mummer mapview sequence are connected by lines of the same color. The match lists produced by mummer can be used alone to generate alignment dot plots, or can be passed on to the clustering algorithms for the identification of longer non-exact regions of conservation.
These match lists have great versatility because they contain huge amounts of information and can be passed forward to other interpretation programs mummer mapview clustering, analysis, searching, etc. In the mummer mapview sections, a short example is given that demonstrates how to use mummer.
Output will be sorted with -r by default and the [BUFF] column will always refer to the sequence whose positions have been sorted.
SNPs for which the [R] and [Q] mummer mapview are greater than 0 should be evaluated with caution, as these columns specify the number of other alignments which overlap this position.
The rectangles connected by lines are maximal exact matches between two sequences, however only the red rectangles would be included in the LIS because they form the longest increasing subset of matches, i. Note that the empty rectangles will be discarded, even though they probably represent a major rearrangement between the two sequences.
Because of this limitation gaps is best suited for the comparison of near identical sequences with the goal of finding minor mutations like SNPs and small indels. The strange syntax is a result of a legacy issue mummer mapview in the Known problems section, and requires the header be stripped from the mummer output.
In addition, gaps is only designed to handle a single reference and a single query sequence, thus the preceding mummer run must also follow this constraint.
The MUMmer 3 examples
The -r is optional and designates the incoming matches as reverse complement matches which must reference mummer mapview reverse complement of the sequence, therefore forcing mummer to be run without the -c option. Please refer to the run-mummer1 script for an example of how to use this program in an alignment pipeline.
Output format The stdout output of gaps shares much in common with the standard three column match output, with the addition of three extra columns: Where the first line is the location of mummer mapview reference file, and the first three columns are the same as the three column match format described in the mummer section.
The final three columns are the overlap between this match and the previous match, the gap between the start of this match and the end of the previous match in the reference, and the gap between the start of this match and the end of the previous match in the query respectively.
A couple suggestions on how to visually scan through this output: The Wrap around list is for circular genomes where the consistent set of matches wraps around the origin of the reference, and the Other matches list shows the matches that were not included in the LIS like the white boxes in the above image.
Finally, if the -r was passed on the command line the Consistent matches and Other matches headers would contain the reverse keyword after the reference file.
Unlike gaps, mgaps is a full clustering algorithm that is capable of generating multiple groups of consistently ordered matches. Clustering is controlled by a set of command-line parameters that adjust the minimum mummer mapview size, maximum gap between matches, etc.
Index of /examples/bioinformatics/mummer
Only matches that were included in clusters will appear in the output, so by adjusting the command-line parameters it is possible to filter mummer mapview many of the spurious matches, thus leaving only the larger areas of conservation between the input sequences.
The major advantage of mgaps is its ability to identify these "islands" of conservation. This frees the user from the single LIS restraints of the gaps program and allows for the identification of large-scale rearrangements, duplications, gene families and so on.
To further illustrate the purpose of this program, consider once again the following set of MUMs illustrated as line connecting two rectangles between two sequences: Just like before the rectangles connected by lines are maximal exact matches between two mummer mapview, with each distinct cluster having its own unique color.
In the previous demonstration using this MUM set, gaps failed to identify the blue cluster because it was not consistent with the LIS. However, by using mgaps, all regions of conservation have now been identified.
The only fallback being the increased complexity of the output, where you once had only one cluster for the whole comparison, you now have four. Because of this, it can sometimes be difficult separating the repetitive clusters from "correct" clusters, making mgaps more suited for global alignments instead of localized error detection.