Genome Analysis Software Site

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IMC O07 Drawing Local Genome Rearrangement Map

What is a local genome rearrangement map?

  • The local genome rearrangement map (Local Genome Rearrangement Map) is one of the functions to compare two 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.
IMC_5.0.9_BZ02_004.JPG

Drawing example of local genome rearrangement map

  • Figure A: Entire genomic map of two closely related genomes (Buchnera 2 species)
  • The feature lane far from the central array lane is the reference genome.
  • The feature lane close to the middle array lane is the comparison target genome.
  • IMC_5.0.6_BX15017.JPG

Figure B: Partial expansion map of two closely related genomes (Buchnera 2 species)

  • The feature lane far from the central array lane is the reference genome.
  • The feature lane close to the middle array lane is the comparison target genome.。
    • IMC_5.0.6_BX15018.JPG

Features and features

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 discrepancies 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 result can be saved and re-browsed as GenBank format file of reference genome

  • LGRM display setting can be registered as layout style (LGRM lane).

You can customize comparison display of base sequence and amino acid sequence

  • LGRM reads ordinary array lane for LGRM and uses it.

 

  • IMC_5.0.6_BX15036.JPG
  • Forward Strand for Amino Acid Display First Frame |
  • Amino acid residue display region of the comparison target genome. Matching bases can be set to hide. In addition, it is possible to switch so that matched bases are displayed with letters / symbols and designated colors.
  • Forward Strand 2nd frame for amino acid display |
  • Amino acid match / mismatch character display area. You can set the characters and symbols to be displayed and their display colors when they match or do not match.
    • : Forward Strand 3rd frame for amino acid display | Amino acid residue display region of comparative genome
    • : Space | base display area of ​​the reference genome (non-display selectable when matching)
    • : Forward Strand base | Forward Strand base display region of reference genome
    • : Center Line |
    • : Reverse Strand base | Forward Strand base display region of reference genome
    • : Space | base display area of ​​the comparison target genome (non-display selectable at the time of matching)
    • : Reverse Strand 1st Frame for Amino Acid Display | Amino Acid Residue Display Region of the Reference Genome
    • : Reverse Strand 2nd frame for amino acid display | amino acid matching / inconsistency character display area. You can set the characters and symbols to be displayed and their display colors when they match or do not match.
    • : Reverse Strand 3rd Frame for Amino Acid Display | Amino Acid Residue Display Area of ​​Comparative Genome. Matching bases can be set to hide. In addition, it is possible to switch so that matched bases are displayed with letters / symbols and designated colors.
  • It is possible to print and output image files as Feature Map
  • It is possible to output array lane part file

Restrictions

This function is implemented in IMC Genomics / Array Edition.

  • As this is a comparison of base sequences, this analysis may not be mostly aligned by non-related genomic analyzes.

 

  • The map is the alignment of homologous regions of the corresponding closely related species genome on the reference genome.
  • Comparative genomic information is written on the reference genome file analyzed by LGRM. It is recommended that you use the alias replicated file in advance as the reference genome.

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