This page links to HTML versions of the alignments as described in the paper. Some additional alignments were
created using more conservative (length) parameter settings in order to reduce potentially occuring artifacts.
When viewing the alignments you will notice that dots '.' appear together with the usual bases A, C, G and T as well as the gap '-' character. Dots may appear in every sequence but the first one. Whenever there is a dot in aligned sequence k > 1 it means the aligned base in this position is the same as the base of the first sequence in the same position. That is, sequence 1 is taken as a reference. Consequently, the alignment of a match (100% identity) is represented by dots in every but the first sequence. The aim of this representation is to enhance readability of the alignments.
Sets of Two Genomes / Genomic Sequences
- Human/Mouse - two genomic sequences from Homo sapiens and Mus muculus
- Mycoplasma - the complete genomes of Mycoplasma pneumoniae and Mycoplasma genitalium
- Tuberculosis - the complete genomes of two strains of Mycobacterium tuberculosis
- Tuberculosis* - same as above, using MEMs instead of MUMs, aligning arbitrarily long gaps up to a distance of 1000
note: the converage is higher but also the number of gaps; most gaps are actually SNPs which fall below the (default) 60% identity threshold - Streptococcus - the complete genomes of two strains of Streptococcus pneumoniae
- E. coli 2 - the complete genomes of two strains of Escherichia coli
Sets of Multiple Genomes
- Adenovirus 6 - six complete genomes of human adenoviruses
- Adenovirus 6* - same as above, using minimal length of 5 instead of 4
- E. coli 3 - the complete genomes of three strains of Escherichia coli
- C. pneumoniae 3 - the complete genomes of three strains of Chlamydophila pneumoniae
- C. pneumoniae 3* - same as above, using minimal length of 5 instead of 4
- S. aureus 3 - three complete genomes of Staphylococcus aureus
- S. aureus 4 - four complete genomes of Staphylococcus aureus
How To Create HTML Pages With Alignments
First run MGA with the additional option -xml to generate XML output. Then call the Perl script mga2html by
Janina Reeder on the resulting XML file. The tool will create HTML pages containing the alignments. You
are free to download and modify the script according to your needs. To run it you need to have installed
Perl 5.6.1 (or newer), the Perl module XML::LibXML 1.52 (or newer) and the gnome libxml2 C-library. Beware
that the script may allocate much main memory and may require much computation time. You can reduce the time
by a considerable amount if you are willing to sacrifice coloured alignments. To do so, specify option -nocolour.
Also, option -format 0 speeds up the computation. But using this option is less recommended, as every alignment
will then be output into a single long line.
