What is the file .mums created by mummer ?
Hello !
I am doing genome sequence alignment using MUMmer, in particular I want to do a dotplot with mummerplot. So the passages that I did are:
1. create a file .mums with the following command line:
mummer -mum -b -c H_pylori26695_Eslice.fasta H_pyloriJ99_Eslice.fasta > mummer.mums
2. and then plot all the MUMs with MUMmerplot:
mummerplot -x "[0,275287]" -y "[0,265111]" -postscript -p mummer mummer.mums
The example is taken here https://mummer4.github.io/tutorial/tutorial.html. The plot works, but I would like to understand several things to have more consciousness of what I am doing: the file .mums has three columns with many values. What do they represent ? I know that it is a little explained in the link given before:
This command will find all maximal unique matches (-mum) between the reference and query on both the forward and reverse strands (-b) and report all the match positions relative to the forward strand (-c). Output is to stdout, so we will redirect it into a file named mummer.mums. This file lists all of the MUMs of the default length or greater between the two input sequences.
So the file should report all the Maximal Unique Matches between the two sequences but I do not understand what are these three columns...
Moreover, can someone explain in simple words the reason of the term "unique" in "Maximal Unique Matches" ?
Thank you in advance .
I am doing genome sequence alignment using MUMmer, in particular I want to do a dotplot with mummerplot. So the passages that I did are:
1. create a file .mums with the following command line:
mummer -mum -b -c H_pylori26695_Eslice.fasta H_pyloriJ99_Eslice.fasta > mummer.mums
2. and then plot all the MUMs with MUMmerplot:
mummerplot -x "[0,275287]" -y "[0,265111]" -postscript -p mummer mummer.mums
The example is taken here https://mummer4.github.io/tutorial/tutorial.html. The plot works, but I would like to understand several things to have more consciousness of what I am doing: the file .mums has three columns with many values. What do they represent ? I know that it is a little explained in the link given before:
This command will find all maximal unique matches (-mum) between the reference and query on both the forward and reverse strands (-b) and report all the match positions relative to the forward strand (-c). Output is to stdout, so we will redirect it into a file named mummer.mums. This file lists all of the MUMs of the default length or greater between the two input sequences.
So the file should report all the Maximal Unique Matches between the two sequences but I do not understand what are these three columns...
Moreover, can someone explain in simple words the reason of the term "unique" in "Maximal Unique Matches" ?
Thank you in advance .
