How were the different genome annotations merged?
The annotations were merged using a combination of all existing described equivalences. As such, the equivalence between gene identifiers described by WaspAtlas is only as accurate as these mappings and due care should be taken when converting between identifiers. The OGS1 equivalence values in the EvidentialGene dataset GFF were used to map these genes to their OGS v1.2 equivalents, and the refseq2 (quality1) values were used to map them to their equivalents in the NCBI Nvit_2.0 (archive) dataset. In both NCBI datasets (NCBI Nvit_2.0 (archive), NCBI Annotation release 101 (latest, mapped to genome build Nvit_2.1)), the NASONIABASE: detail in the GFF files was used to map these genes to their OGS v1.2 equivalents. The two NCBI sets were inter-mapped using the gene name attribute.
Why are two separate NCBI annotations shown?
In WaspAtlas, we show two NCBI annotations: NCBI Annotation release 101
(mapped to Nvit_2.1 is the most recent annotation, and NCBI (archived Nvit_2.0 annotation)
is an outdated one. Rather than simply opting to show the most recent one, we understand that many studies may have used previous annotations such as this in their analysis and thus genome co-ordinates, etc, may only map onto this version of the annotation. To allow us to capture as much work as possible into each gene, we thus opted to show both versions.
How were the gene ontology (GO) terms annotated?
(GO) term annotations were taken from several sources. Firstly, we took the GO terms from Ensembl as annotated onto OGS v1.2. Secondly, we used the blast2go DAT file
provided by NasoniaBase
to map GO terms onto the EvidentialGene dataset. Thirdly and finally, we calculated Drosophila melanogaster
orthologs (a combination of Ensembl annotated orthologs and a reciprocal best blast hit protein search), and merged all annotated GO terms (Ensembl) for the Drosophila
orthologs into our database.
How can I submit my data for inclusion into WaspAtlas?
We are currently working on an automated submission system, but if you would like us to include your data in WaspAtlas for others to browse before this is released, please send an e-mail to firstname.lastname@example.org.
Genome annotations used in WaspAtlas were produced by NasoniaBase  (All datasets) and have been further annotated by Ensembl  (Official gene set v1.2) and NCBI  (Nvit_2.0 archived annotation & Nvit_2.1 annotation release 101). GO annotations  were assigned in part by NasoniaBase using blast2go . PFAM  domains were predicted using HMMER
. WaspAtlas was developed using Catalyst
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