Local Genome Rearrangement Analysis
What is a local genome rearrangement map?
The local genome rearrangement map (Local Genome Rearrangement Map) is one of the functions to compare closely related species. A comparison of homology regions along the maximum homology path between two genomes is displayed at the base sequence and amino acid sequence level and annotations on those genomes are displayed.
Detect homologous regions with different closely related genomes on the reference genome and draw a local genomic rearrangement map in which the nucleotide sequence and the features of each genome are aligned. I call this function the local genome rearrangement map.
We create and draw a local genomic rearrangement map across the two closely related species.
For the reference genome, we map the entire genomes of closely related species to be compared.
It displays the homologous region at the base sequence level throughout the genome between the two genomes.
In the coding region, corresponding amino acid residues are aligned.
You can move the map to the corresponding position by listing the mismatch points of amino acid residues and clicking on each mismatch point in the list.
A list of coincident parts and residues can be output as a CSV file.
The list will be reproduced and displayed when reloading.
In the homologous region, the features of both genomes and their positions are aligned.
For regions where there is no homology with the reference genome, the features of the comparison genome will not be displayed.
This is judged from the principle that the LGRM maps the comparison genome to the reference genome, as a region which is not mapped, that is, a region deleted from the comparison target genome.
Analysis results can be saved and re-browsed as GenBank format files of the reference genome.
LGRM display setting can be registered as layout style (LGRM lane).
The LGR Map lane can be placed at any position in the main feature map.
You can customize comparison display of base sequence and amino acid sequence
LGRM reads ordinary array lane for LGRM and uses it.