Genome Comparison
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- Multiple genome alignment / feature map
- Homology search between chromosomes
- Feature alignment, gene cluster alignment
- Circular genome map (corresponding to feature layout style)
- Dot plot
- Global genome rearrangement mapping (global genome rearrangement map)
- Local genome rearrangement mapping (local genome rearrangement map)
- Venn Diagram (Venn Diagram): for ortholog analysis
- Repetitive sequence detection
- Metagenome analysis by 16S rRNA from next generation sequencer
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Subcategories
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Function to draw the feature and the composition of more than one related species genome in parallel on the concentric-circle.
The addendum - the manipulation - a circular lane can be freely deleted from the drawing DIALOG.
It is the designation only of the designation feature content imaging order alteration GenomeMap designation assignment feature in the content skew of the judgement of the chromosome base-sequence of more than one designation in the feature of the judgement of the chromosome base-sequence with more than one annotation.
Independent color setting by the concentric-circle.
It subscribes a layout style and in the circular genome map of a lot of genomes, efficiently, this creation circular genome map graphic arts ( the PDF, EMF, PNG )
Implemented Editions:IMCGE and IMCAE.
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This function is installed in the following software
IMCGE
IMCAE
GenomeTraveler
- Multiple Linear Genome Map (Multiple Linear Genome Map) is a function to comparatively draw Feature from multiple genomic chromosomes between closely related species in parallel.
- Homology search can be performed on all the features on other genomes by right clicking one feature on the multiple linear genomic map and if that feature has homologous clan strings on other genomes, homologous genes Alignment can be displayed on the axis.
- "IMC O10 Gene Cluster Alignment" can be executed by right mouse click from multiple linear map.
- You can output files in PDF, PNG, and EMF image formats.
- This function is implemented in the following editions.
- We display homology regions between two genomic sequences in dot matrix.
- Select and compare the current genome sequence and one genomic sequence loaded in the current reference directory.
- You can set dot color by Overlap base length,% Identity level.
- In the result display window, zooming, shifting, enlarging an arbitrary region selected by rectangle, dot color setting, navigation window, restriction on the number of display dots, and feature key display (display of annotations with feature - mouse-over) are possible.
- A dot image can be output as a file in PDF / PNG / EMF format, and print setting is also possible.
- The dot list can be output as a file in CSV format.
Venn Diagram is a diagram used in set theory, showing the distribution of the number of elements between 3 sets (4 or more sets can be drawn, but IMC draws only 3 sets or less) It is.
Elements belonging to each set are shown in the circle, and overlapping parts are shown as common elements.
It is used for biological applications to illustrate the number of orthologous or unique genes between closely related genomes.
Gene cluster alignment focuses on one gene of a plurality of closely related genomes, and includes the vicinity thereof (N gene ranges in the upstream and N gene ranges in the downstream), and the relationship between the closely related species genome
The presence or absence of homology is investigated, and when there is BBH, homologous genes are combined and displayed in bands.
- Detects mutation points between closely related genomes in base units.
- Based on the current genome sequence, you can select and compare two or more from the genomic sequence loaded in the current reference directory.
- The genomic sequence must be genetically extracted and the CDS feature must be registered.
- The detection site can be set on CDS or intergenic region. For detection criteria, you can change% Identity and Overlap rate.
- A list of mutated bases is displayed on the analysis result screen, and the display items are mutated bases, mutation positions, gene names, ocus-Tags by genome sequence.
- Results can be output in CSV format.