Browser (faqs)

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.

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.

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:

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

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).

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).

Supporting evidence for a transcript

Transcript sources

Answer: 

Transcript sources

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 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.

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.

Pages

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