Data (faqs)

FAQ category.

Are the (genomes) gene sets experimentally validated?

Answer: 

No genes have been experimentally validated by VectorBase, but automatic predictions of the initial gene sets are done using two approaches:

Are the BLAST databases masked?

Answer: 

The

Which are the gene biotype definitions?

Answer: 

This a Search query for all genes in VectorBase (click on the image to enlarge):

How are "high confidence" orthologs defined?

Ortholog metrics are calculated for some groups of species, and these are used to classify a "high confidence" set of orthologs.

Answer: 

Ortholog metrics are calculated for some groups of species, and these are used to classify a "high confidence" set of orthologs.

How are RNA genes annotated?

Answer: 

A large proportion of the RNA genes in VectorBase are annotated in a completely automated way. There are some exceptions to this rule, where we import genes from other sources, or have been supplied with manual annotations for particular classes of RNA.

VectorBase automated annotation

VectorBase uses three sources for RNA gene annotation:

What the gene set counts mean?

Answer: 

This a gene set table (click on the image to enlarge):

Gene set table

What data is available for download?

Answer: 

The data in VectorBase is available for download in a variety of formats.

Is there any plan to map the species supercontigs to chromosomes?

Answer: 
Currently all VectorBase genomes, with the exception of Anopheles gambiae PEST, are available only as supercontigs. For some species, the genome papers and other publications have achieved to locate a subset of the supercontigs.

Is it possible to query for genes' pathway information? e.g., KEGG

Answer: 

KEEG

KEGG is a database to understand high-level functions and utilities of biological systems, from molecular-level information. One of its data-oriented entry points is KEGG pathway, a collection of manually drawn pathway maps representing knowledge on the molecular interaction and reaction networks among proteins and other molecules. These curated pathways include six of our hosted genomes, these species are Aedes aegypti, Anopheles gambiae, Culex quinquefasciatus, Ixodes scapularis, Musca domestica and Pediculus humans.

How are gene descriptions propagated between species?

Some of the species in VectorBase have been annotated more extensively than others, and it is useful to propagate gene descriptions to closely related species. Gene descriptions (but not gene names) are propagated based on orthology.

If there is one-to-one or one-to-many orthology between a gene in a source (i.e. well annotated) species and a target species, then the description is propagated from the source to the target if the following conditions are met:

Answer: 

Some of the species in VectorBase have been annotated more extensively than others, and it is useful to propagate gene descriptions to closely related species. Gene descriptions (but not gene names) are propagated based on orthology.

If there is one-to-one or one-to-many orthology between a gene in a source (i.e. well annotated) species and a target species, then the description is propagated from the source to the target if the following conditions are met:

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