WaspAtlas A Nasonia vitripennis gene database





About WaspAtlas


Contact us

WaspAtlas was developed at the Tauber lab. For information, you may contact Dr Eran Tauber by sending an e-mail to etaubersdfdsfs@univ.haifa.ac.il. Alternatively, the Tauber lab may be contacted through Twitter or Facebook.

Data usage & how to cite

As WaspAtlas is primarily an interface for existing Nasonia vitripennis genome data, please cite the appropriate curating body for usage of genome annotation data. Data from other studies should cite the original publication. WaspAtlas itself can currently be cited as:

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

See the references section for more details.

FAQs

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Annotation release 101 (mapped to Nvit_2.1 is the most recent annotation, and NCBI (archived Nvit_2.0 annotation) is an outdated one.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?

Gene ontology (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 et22sdfdsfs@le.ac.uk.

References

Genome annotations used in WaspAtlas were produced by NasoniaBase [4][7] (All datasets) and have been further annotated by Ensembl [6] (Official gene set v1.2) and NCBI [5] (Nvit_2.0 archived annotation & Nvit_2.1 annotation release 101). GO annotations [4] were assigned in part by NasoniaBase using blast2go [1]. PFAM [2] domains were predicted using HMMER. WaspAtlas was developed using Catalyst.
[1] A. Conesa, S. Götz, J. M. Garcia-Gomez, J. Terol, M. Talon and M. Robles. "Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research", Bioinformatics, Vol. 21, September, 2005, pp. 3674-3676.

[2] Pfam: clans, web tools and services: R.D. Finn, J. Mistry, B. Schuster-Böckler, S. Griffiths-Jones, V. Hollich, T. Lassmann, S. Moxon, M. Marshall, A. Khanna, R. Durbin, S.R. Eddy, E.L.L. Sonnhammer and A. Bateman Nucleic Acids Research (2006) Database Issue 34:D247-D251

[3] The Gene Ontology Consortium. Gene ontology: tool for the unification of biology. Nat. Genet.. May 2000;25(1):25-9.

[4] Munoz-Torres MC, Reese JT, Childers CP, Bennett AK, Sundaram JP, Childs KL, Anzola JM, Milshina N, Elsik CG. 20011. Hymenoptera Genome Database: integrated community resources for insect species of the order Hymenoptera. Nucleic Acids Research 39: D658-D662.

[5] The NCBI handbook [Internet]. Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information; 2002 Oct. Chapter 18, The Reference Sequence (RefSeq) Project. Available from http://www.ncbi.nlm.nih.gov/books/NBK21091/

[6] Paul Flicek, M. Ridwan Amode, Daniel Barrell, Kathryn Beal, Konstantinos Billis, Simon Brent, Denise Carvalho-Silva, Peter Clapham, Guy Coates, Stephen Fitzgerald, Laurent Gil, Carlos García Girón, Leo Gordon, Thibaut Hourlier, Sarah Hunt, Nathan Johnson, Thomas Juettemann, Andreas K. Kähäri, Stephen Keenan, Eugene Kulesha, Fergal J. Martin, Thomas Maurel, William M. McLaren, Daniel N. Murphy, Rishi Nag, Bert Overduin, Miguel Pignatelli, Bethan Pritchard, Emily Pritchard, Harpreet S. Riat, Magali Ruffier, Daniel Sheppard, Kieron Taylor, Anja Thormann, Stephen J. Trevanion, Alessandro Vullo, Steven P. Wilder, Mark Wilson, Amonida Zadissa, Bronwen L. Aken, Ewan Birney, Fiona Cunningham, Jennifer Harrow, Javier Herrero, Tim J.P. Hubbard, Rhoda Kinsella, Matthieu Muffato, Anne Parker, Giulietta Spudich, Andy Yates, Daniel R. Zerbino, and Stephen M.J. Searle. Ensembl 2014. Nucleic Acids Research 2014 42 Database issue:D749-D755

[7] Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK; Nasonia Genome Working Group. 2010. Functional and evolutionary insights from the genomes of three parasitoid Nasonia species. Science 327: 343-348.