Browser (faqs)

Individual genotypes

For the top panel describing variation details such as source and class, see this help page.

Tables of genotype information are shown. Number of genotypes (individuals), populations, and descriptions appear by default, in the table. To see the list of all individuals in a population, click the Show link. Individuals and specific genotypes will be revealed.

Answer: 

For the top panel describing variation details such as source and class, see this help page.

Tables of genotype information are shown. Number of genotypes (individuals), populations, and descriptions appear by default, in the table. To see the list of all individuals in a population, click the Show link. Individuals and specific genotypes will be revealed.

Population genetics

For the top panel describing variation details such as source and class, see this help page.

Answer: 

For the top panel describing variation details such as source and class, see this help page.

Alignments (Image)

The top panel is similar to the gene map shown in the Region in Detail view in the Location tab.

Answer: 

The top panel is similar to the gene map shown in the Region in Detail view in the Location tab.

Genomic alignments view

Whole genome aligments include "pairwise" sequence alignments between two species, and multi-species alignments using genomes of more than two species.

Export alignments with the Export data link in the left hand navigation column of the "Genomic alignments" page.

The sequence is centered on one gene. To change the sequence shown, use a different gene or click on "genomic alignments" from the location tab.

The Display

Answer: 

Whole genome aligments include "pairwise" sequence alignments between two species, and multi-species alignments using genomes of more than two species.

Export alignments with the Export data link in the left hand navigation column of the "Genomic alignments" page.

The sequence is centered on one gene. To change the sequence shown, use a different gene or click on "genomic alignments" from the location tab.

The Display

Paralogues view

Homologues are inferred from the gene trees, which are determined using all species in VectorBase. A detailed description of the method is provided here.

Paralogues are defined as genes for which the most common ancestor node is a duplication event. These ancestral duplications are represented by red nodes in the gene trees.

Answer: 

Homologues are inferred from the gene trees, which are determined using all species in VectorBase. A detailed description of the method is provided here.

Paralogues are defined as genes for which the most common ancestor node is a duplication event. These ancestral duplications are represented by red nodes in the gene trees.

Linkage disequilibrium data

This view displays detailed information about linkage disequilibrium (LD) that measures the correlation between two alleles (neighbouring genetic variations) in a specific population.Two values have been calculated:

  • r2
  • D'

Note that only LDs with r2 values larger than 0.05 are available.

Answer: 

This view displays detailed information about linkage disequilibrium (LD) that measures the correlation between two alleles (neighbouring genetic variations) in a specific population.Two values have been calculated:

  • r2
  • D'

Note that only LDs with r2 values larger than 0.05 are available.

Population comparison

This help page is for both the population comparison table and comparison image. Variation sources are described in this document.

Answer: 

This help page is for both the population comparison table and comparison image. Variation sources are described in this document.

Resequencing alignments

This view compares sequences across individuals (human), breeds, or strains.

The first line of sequence is the reference genome. Subsequent lines of sequence are genomes for other individuals, breeds, or strains. A dot signifies the same nucleotide as the reference sequence at that position. The view can be customised to show the nucleotide rather than a dot (see next paragraph). A tilde, or squiggle, signifies a lack of resequencing coverage at that position.

Answer: 

This view compares sequences across individuals (human), breeds, or strains.

The first line of sequence is the reference genome. Subsequent lines of sequence are genomes for other individuals, breeds, or strains. A dot signifies the same nucleotide as the reference sequence at that position. The view can be customised to show the nucleotide rather than a dot (see next paragraph). A tilde, or squiggle, signifies a lack of resequencing coverage at that position.

Oligo probes

Probesets from microarray platforms are matched to genes according to the 2-step mapping procedure.

Note: probesets can only be mapped if the sequences are provided to Vectorbase by the manufacturer.

You can export oligo probe mappings for several genes or transcripts using the BioMart tool. Watch a tutorial video to learn how to use BioMart.

Answer: 

Probesets from microarray platforms are matched to genes according to the 2-step mapping procedure.

Note: probesets can only be mapped if the sequences are provided to Vectorbase by the manufacturer.

You can export oligo probe mappings for several genes or transcripts using the BioMart tool. Watch a tutorial video to learn how to use BioMart.

Gene/protein tree

VectorBase gene trees are generated by the Gene Orthology/Paralogy prediction method pipeline. All homologues are determined from gene trees.

Gene trees are constructed using one representative protein for every gene in every species. (They can also be considered as protein trees).

Answer: 

VectorBase gene trees are generated by the Gene Orthology/Paralogy prediction method pipeline. All homologues are determined from gene trees.

Gene trees are constructed using one representative protein for every gene in every species. (They can also be considered as protein trees).

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