Browser (faqs)

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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.

Alignments (Text)

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.

Sequence 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.

Sequence Display

lawson's picture

cDNA sequence

Example page

This highly customisable sequence shows, by default, the transcript sequence (cDNA), the coding sequence underneath it, and the protein sequence in the third line. Line numbering is different for all three sequences.

Line numbering

Answer: 

Example page

This highly customisable sequence shows, by default, the transcript sequence (cDNA), the coding sequence underneath it, and the protein sequence in the third line. Line numbering is different for all three sequences.

Line numbering

Chromosome

A zoomed-in view of a chromosome is shown, including graphical displays of known and novel genes, percent of GC repeats, and variation density. Click on the chromosome to zoom in to Region in Detail. Add your own annotation to one chromosome, or a

Answer: 

A zoomed-in view of a chromosome is shown, including graphical displays of known and novel genes, percent of GC repeats, and variation density. Click on the chromosome to zoom in to Region in Detail. Add your own annotation to one chromosome, or a

Exons - Sequence view

Exons, introns and flanking sequence are shown for one

Answer: 

Exons, introns and flanking sequence are shown for one

Explore this variation

This page offers a top panel of information specific to the variant. Graphical icons are presented that lead you to more specific variant data, also accessible from the links at the left. The links in the left hand menu have a corresponding icon. It's your choice how to navigate through the variation displays.

Top Panel

From the top of the view, the following information can be found:

Answer: 

This page offers a top panel of information specific to the variant. Graphical icons are presented that lead you to more specific variant data, also accessible from the links at the left. The links in the left hand menu have a corresponding icon. It's your choice how to navigate through the variation displays.

Top Panel

From the top of the view, the following information can be found:

External data

Databases and projects external to VectorBase can be shown here. Click Configure this page to choose what information to view, related to your gene of interest. This page uses DAS or the Distributed Annotation System to show biological annotation from other sources. You can upload your own data (click on Configure this page, use the Custom Data tab).

Answer: 

Databases and projects external to VectorBase can be shown here. Click Configure this page to choose what information to view, related to your gene of interest. This page uses DAS or the Distributed Annotation System to show biological annotation from other sources. You can upload your own data (click on Configure this page, use the Custom Data tab).

External references

Genes, transcripts, and proteins are matched to sequences and information in other biological databases. The matches are referred to as external references, or Xrefs.

Xref sources for VectorBase genes include UniProtKB, EntrezGene, PubMed & Community symbols/descriptions.

Answer: 

Genes, transcripts, and proteins are matched to sequences and information in other biological databases. The matches are referred to as external references, or Xrefs.

Xref sources for VectorBase genes include UniProtKB, EntrezGene, PubMed & Community symbols/descriptions.

Gene ontology

Answer: 

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).

General identifiers

Genes, transcripts, and proteins are matched to sequences and information in other biological databases. The matches are referred to as external references, or Xrefs, in the Ensembl API.

Answer: 

Genes, transcripts, and proteins are matched to sequences and information in other biological databases. The matches are referred to as external references, or Xrefs, in the Ensembl API.

Gene summary

Listed at the top of this page are the gene symbol, name, source of the name, and location (in chromosome and base pairs). The gene name refers to the symbol extracted from publications or submitted directly by the community.

VectorBase IDs use a four-letter code to represent the species and strain information e.g. 'AGAP' for Anopheles gambiae. The 6-digit number following each ID is unique for that gene, and stable (unchanging), unless the gene model drastically changes.

Answer: 

Listed at the top of this page are the gene symbol, name, source of the name, and location (in chromosome and base pairs). The gene name refers to the symbol extracted from publications or submitted directly by the community.

VectorBase IDs use a four-letter code to represent the species and strain information e.g. 'AGAP' for Anopheles gambiae. The 6-digit number following each ID is unique for that gene, and stable (unchanging), unless the gene model drastically changes.

Genome sequence

This page shows the genome sequence for a gene of interest. Flanking sequence and introns are displayed. Exons belonging to the gene of interest are shown in red letters with red highlighting. Other exons within this region that do not belong to the gene of interest are shown in black letters with red highlights. Note that coding and non-coding transcripts contribute to this view.

Answer: 

This page shows the genome sequence for a gene of interest. Flanking sequence and introns are displayed. Exons belonging to the gene of interest are shown in red letters with red highlighting. Other exons within this region that do not belong to the gene of interest are shown in black letters with red highlights. Note that coding and non-coding transcripts contribute to this view.

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

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.

Is there a list of all pairwise alignments?

The list of all pairwise alignments in VectorBase includes a link to coverage statistics for each alignment (e.g. Anopheles gambiae and Anopheles coluzzii) and a link to an example region (e.g.

Answer: 

The list of all pairwise alignments in VectorBase includes a link to coverage statistics for each alignment (e.g. Anopheles gambiae and Anopheles coluzzii) and a link to an example region (e.g.

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.

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.

Orthologues view

Answer: 

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.

Phenotype data

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

Diseases and traits that are associated with the variation of interest are shown on this page. The sources of these associations are listed in the second column and include:

Answer: 

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

Diseases and traits that are associated with the variation of interest are shown on this page. The sources of these associations are listed in the second column and include:

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.

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.

Protein - Sequence

A protein sequence corresponding to one transcript is shown. For more isoforms and splice variants, go to the Gene Summary view by clicking on the Gene tab.

Answer: 

A protein sequence corresponding to one transcript is shown. For more isoforms and splice variants, go to the Gene Summary view by clicking on the Gene tab.

Protein summary

One protein is shown as a purple bar, with alternating shades of light and dark purple reflecting alternating exons. Below that, domains and motifs from multiple projects are mapped along the protein. Click on any motif to find the corresponding amino acid positions on the protein, along with

Answer: 

One protein is shown as a purple bar, with alternating shades of light and dark purple reflecting alternating exons. Below that, domains and motifs from multiple projects are mapped along the protein. Click on any motif to find the corresponding amino acid positions on the protein, along with

Region comparison

The top panels are similar to the chromosome diagram and gene map at the top of the Region in Detail view in the Location tab. More than one species can be compared in the panels.

Answer: 

The top panels are similar to the chromosome diagram and gene map at the top of the Region in Detail view in the Location tab. More than one species can be compared in the panels.

Region in detail

Follow these links for example pages:

Answer: 

Follow these links for example pages:

Region overview

A customisable, zoomed-out region of a 1MB or higher region of the chromosome (compared with Region in Detail which limits to a 1MB region or less). Genes and structural variations are shown by default. Other data tracks can be added using the Configure this page tool button at the left.

Answer: 

A customisable, zoomed-out region of a 1MB or higher region of the chromosome (compared with Region in Detail which limits to a 1MB region or less). Genes and structural variations are shown by default. Other data tracks can be added using the Configure this page tool button at the left.

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.

Splice variants

This view shows all spliced transcripts for a gene, including EST transcripts and ncRNAs (non-coding RNAs).

Answer: 

This view shows all spliced transcripts for a gene, including EST transcripts and ncRNAs (non-coding RNAs).

Structural variation

Structural variants are imported from publications and from personal communications from the community (Igor Sharakov). They are drawn along the genome (blue bar).

Below the graphical view, the structural variants in the gene region are provided as a table.

Answer: 

Structural variants are imported from publications and from personal communications from the community (Igor Sharakov). They are drawn along the genome (blue bar).

Below the graphical view, the structural variants in the gene region are provided as a table.

Supporting evidence for a transcript

Transcript sources

Answer: 

Transcript sources

Transcript ID history

Stable gene, transcript, and protein identifiers are kept the same throughout VectorBase releases unless the gene or transcript model changes dramatically. In this case, the old stable identifier may be retired and a new one assigned (or two identifiers may be merged into one).

Answer: 

Stable gene, transcript, and protein identifiers are kept the same throughout VectorBase releases unless the gene or transcript model changes dramatically. In this case, the old stable identifier may be retired and a new one assigned (or two identifiers may be merged into one).

Transcript summary

TRANSCRIPT TABLE

The table shows all splice variants for a gene and includes noncoding transcripts.

The transcript which you are viewing is highlighted in blue in the table.

Answer: 

TRANSCRIPT TABLE

The table shows all splice variants for a gene and includes noncoding transcripts.

The transcript which you are viewing is highlighted in blue in the table.

What styles are available for the data tracks in the Genome Browser?

Answer: 

Whole genome

A

Answer: 

A

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