StellaBase: Nematostella vectensis Genomics Database
 

INDEX

Version / Release Information

The current version of StellaBase is '1.0'. This version of StellaBase utilizes a an assembly of the genome produced by Phusion Assembly Software. Pfam Models release 18 and HMM Program release 2.3.2 were used to search this assembly. Changes as a function of updates to these programs / databases can be tracked through the version numbers posted on this page.

Development of StellaBase

StellaBase is the Nematostella vectensis genomics database. This communtiy resource was developed by members of the Finnerty Laboratory at Boston University (Jim Sullivan, Joe Ryan, John Finnerty) and collaboraters including Dan Rokshar (Joint Genomes Institute), Jim Mullikin (National Genome Research Institute), and Jim Watson and Jeramy Webb (Boston University). The Nematostella image used in the html for this database was devised and created by graphical designer Darryl Leja (National Institute of Health). This research was funded by the National Science Foundation (grant IBN-0212773 to J. Finnerty) and by the Intramural Research Program of the National Human Genome Research Institute, National Institutes of Health.

The Nematostella genome was sequenced by the Joint Genomes Institute (D. Rokshar). Shotgun traces of the genome were assembled using Phusion (J. Mullikin); genes were predicted from the assembled genome using Genscan. Putative genes were blasted against the entire Pfam library, consisting of 7868 unique protein family motifs, using HMMER.

Accessing Data

Results from Genscan and Hmm predictions and the assembly itself are stored in relational databases and are searchable through this interface using both keyword (Gene Search and Gene family search) and sequence homolgy (StellaBLAST) search functions.

Additionally, CnidBase search functions allow users to compare gene families across divergent taxa searching either by gene family or genome.

Other data stored on StellaBase includes Nematostella gene expression patterns, a primer library, a genetic stock library, and a literature repository. For a comprehensive resource regarding the biology of Nematostella, please visit nematostella.org.

Community Contributions Welcome

StellaBase is a resource for the community, and we welcome community support. Please contact the StellaBase manager with suggestions and comments. We welcome users to submit primers, genetic or living stock, and any available data regarding predicted genes.

Development of species-specific databases

We welcome other reseachers to build sister databases to StellaBase. Our table structure and entity-relationship diagram may be used to replicate our relational database structure. HTML, CGI, and MySQL code for web interface and data querying are available upon request.

Citing StellaBase

If you would like to cite or find out more information about StellaBase see the publication in Nucleic Acids Research

Sullivan JC, Ryan JF, Watson JA, Webb J, Mullikin JC, Rokhsar D, Finnerty JR. StellaBase: The Nematostella vectensis Genomics Database. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D495-9.

Funding

This material is based upon work supported by the National Science Foundation under Grant No. 0212773.

Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

Thank you for using StellaBase. We hope you have found this a helpful resource.

Questions, comments, suggestions: busully@bu.edu