v2.3   
UPDATED 11/2015
Augmented Annotation and Orthologue Analysis for Oryctolagus cuniculus
  FREQUENTLY ASKED QUESTIONS
  1. What browsers does Better Bunny work with?
  2. What kind of identifier (ID) can I search on?
  3. What do I use to separate a list of identifiers?
  4. What Agilent Microarray probe identifiers does Better Bunny work with?
  5. Where does all this additional information come from?
  6. How often is it updated?
  7. What version of the Ensembl database do you use for annotations?
  8. What version of the Agilent rabbit array do you use for annotations?
  9. Where do your gene ontology (GO) terms come from?
  10. Can I get gene ontology (GO) terms just from rabbit?
  11. Where can I find more information on DAVID and functional annotation?

What browsers does Better Bunny work with?
Better Bunny has been tested with the following web browsers:

  Chrome 46.0
  Firefox 42.0
  Internet Explorer 10.0
  Opera 30.0
  Safari 5.0

What kind of identifier (ID) can I search on?
By default the Search page expects a list of Agilent probe IDs. To search using UniGene, Ensembl Gene, Entrez Gene, or NCBI Protein IDs, use the dropdown at the top of the page to select the appropriate type.

To load a sample list of IDs, select the type from the dropdown, then click the SAMPLE IDS button.

What do I use to separate a list of identifiers?
Identifiers may be separated by spaces, comma, carriage-return, or any combination of these three. This is true for both text and file input.

What Agilent Microarray probe identifiers does Better Bunny work with?
Better Bunny accepts probe identifiers for the Agilent Rabbit Gene Expression Microarray

  Product Number: G2519F
  Format: 4 X 44K
  Design ID: 020908
  GPL ID: GPL7083

Where does all this additional information come from?
All added gene description, gene name, GO terms, and orthologue data is periodically downloaded from Ensembl's BioMart. Additional gene and protein identifiers, as well as updated descriptions and gene names, are downloaded from NCBI.

How often is it updated?
Updates to Better Bunny are made whenever Ensembl makes a new release (approximately quarterly), or Agilent updates their probe annotations.

What version of the Ensembl database do you use for annotations?
Better Bunny v2.3 uses Ensembl Genes 82, oryCun2.0 (accessed 20 Oct 2015).

What version of the Agilent rabbit array do you use for annotations?
Better Bunny v2.3 uses the Agilent annotation update for the Rabbit Gene Expression Microarray dated 04 Dec 2014.

Where do your gene ontology (GO) terms come from?
All gene ontology terms are downloaded from Ensembl. The Ensembl database infers most terms for genes from homologous UniProt mappings. That is, most GO terms are inferred from species other than rabbit.

Can I get gene ontology (GO) terms just from rabbit?
For gene ontologies specific to rabbit (i.e., not derived from orthologues) see the Gene Ontology website. To search/browse for rabbit try Gene Ontology AmiGO. Select Browse then choose Oryctolagus cuniculus under species to filter for rabbit.

Where can I find more information on DAVID and functional annotation?
For a step-by-step procedure on using DAVID for gene functional analysis see:

Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources. (2009) Nature Protocols 4(1):44-57