WaspAtlas A Nasonia vitripennis gene database

Latest updates

(7/1/2016) Sequence downloads added

The full transcript sequences, coding sequences, and UTR sequences for all Nasonia vitripennis transcripts in WaspAtlas are now all available in the downloads section of the website.

(3/11/2015) Ortholog retrieval tool added

A tool for retrieving Nasonia orthologs for lists of genes from supported species has been added to the tools section of the website.

(20/10/2015) Conserved region data added to WaspAtlas

Data concerning upstream non-coding conserved regions has been added to WaspAtlas and can be browsed here:

CNE browser

The publication relating to this data has been published in BMC Evolutionary Biology:
(Davies et al, 2015).

(20/10/2015) WaspAtlas published!

WaspAtlas has been published in Database and can be cited here:

Nathaniel J. Davies and Eran Tauber
WaspAtlas: a Nasonia vitripennis gene database and analysis platform
Database 2015: bav103 doi:10.1093/database/bav103 published online October 9, 2015

We thank the anonymous reviewers for their comments and suggestions on improving both WaspAtlas and the publication.

(20/10/2015) Bug fix to tools section

A bug in the GO/PFAM overrepresentation tool has been fixed which caused slight overestimations of k in cases where unannotated genes were included in the test dataset. Analyses conducted using this tool before this date (20/10/2015) should be double-checked to ensure that this bug does not alter results.

(29/8/2015) Genome browser added

The Nasonia vitripennis genome browser has been added to WaspAtlas, allowing users to browse gene neighbourhoods and view splice variants. All four annotation datasets have been included, and the browser has been fully interlinked with other pages on the website.

The browser is powered by Genoverse and can be accessed here.

(8/7/2015) Developmental gene expression data added

Tiling microarray data showing developmental expression in N. vitripennis females produced by Xu Wang et al has been integrated into WaspAtlas. This data was generated for OGS2 (Evidential gene dataset).

The publication relating to the data can be found in PLOS Genetics:
Function and Evolution of DNA Methylation in Nasonia vitripennis

(6/7/2015) WaspAtlas v2.1 released!

This release of WaspAtlas integrates data from several Nasonia vitripennis RNA-seq datasets, allowing users to compare expression levels of genes across sexes and tissues. Similarly to FlyAtlas, WaspAtlas provides expression enrichment scores relative to whole-body samples in both sexes. The expression values have been calculated for the NCBI Nvit v2.1 annotation. All of the inter-annotation set mappings remain the same as in WaspAtlas v2.0.

(2/3/2015) WaspAtlas v2.0 released!

Welcome to the new version of WaspAtlas!

This release combines data from all available Nasonia vitripennis genome annotations to provide a gene-based view of the N. vitripennis genome, allowing users to view transcript information & sequences, protein products, GO annotations, PFAM protein domain predictions, and much more. All genome annotations used have been mapped to each other (more information) and so identifiers from one annotation may be converted to identifiers from another annotation, allowing comparison of studies which are based on different gene annotations. We also provide a set of tools for working with N. vitripennis, currently including RNAi off-target prediction, and gene ontology/PFAM domain hypergeometric overrepresentation tests.

As WaspAtlas allows for the integration of empirical data relating to each gene, we encourage authors of such work to submit their data to WaspAtlas so that it may be made easily available to the scientific community. We at the Tauber lab intend to integrate our own data into the website, including methylation and expression (RNA-seq and in-situ hybridisation) data.

(2/3/2015) RRBS methylation data added - Tauber lab

"Seasonal photoperiodic changes have strong impact on development on Nasonia vitripennis. Here, Using high-throughput Reduced Representation Bisulfite Sequencing (RRBS), we have generated DNA methylation maps of female wasps maintained in long vs short day. We have identified differentially methylated loci that encode the photoperiodic change."

The manuscript relating to this data is currently under review.

This data has been made available (pre-publication) on WaspAtlas and can be viewed in the "Studies" section for each gene. The full dataset has been archived here, and is released under the NIH/NHGRI policy for Release and Database Deposition of Sequence Data. If you wish to perform large-scale genomic analyses using this data, please first contact the Tauber lab.