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Drospege: Rapid Access Database for New Drosophila Species Genomes Donald G D480–D485 Nucleic Acids Research, 2007, Vol. 35, Database issue doi:10.1093/nar/gkl997 DroSpeGe: rapid access database for new Drosophila species genomes Donald G. Gilbert* Department of Biology, Indiana University, Bloomington, IN 47405, USA Received September 15, 2006; Revised October 17, 2006; Accepted October 20, 2006 ABSTRACT have rapid access to these new genomes, including basic annotations from well-studied model organisms and The Drosophila species comparative genome predictions to locate potential new genes, to make sense of database DroSpeGe (http://insects.eugenes.org/ them. Genome annotation and database management can be DroSpeGe/) provides genome researchers with streamlined now using generic tools, shared computing rapid, usable access to 12 new and old Drosophila resources and common genome database techniques to Downloaded from genomes, since its inception in 2004. Scientists can provide useful access to biologists in weeks instead of use, with minimal computing expertise, the wealth several months. of new genome information for developing new New genome sequencing projects and communities are insights into insect evolution. New genome assem- facing large informatics tasks for incorporating, curating and annotating and disseminating sequence and annotation blies provided by several sequencing centers have http://nar.oxfordjournals.org/ been annotated with known model organism gene data. Effective genome studies need an informatics infra- structure that moves beyond individual organism projects homologies and gene predictions to provided basic to a cost-effective use of common tools. Expertise from comparative data. TeraGrid supplies the shared existing genome projects should be leveraged into building cyberinfrastructure for the primary computations. such tools. The Generic Model Organism Database [GMOD This genome database includes homologies to (3)] project has this goal, to fully develop and extend a gen- Drosophila melanogaster and eight other eukaryote ome database tool set to the level of quality needed to create model genomes, and gene predictions from several and maintain new genome databases. GMOD and related gen- groups. BLAST searches of the newest assemblies ome database tools now support a portion of the basic tasks by guest on November 14, 2015 are integrated with genome maps. GBrowse maps for such. Two needs in development for GMOD are the cre- provide detailed views of cross-species aligned ation of new databases for emerging model organisms, and genomes. BioMart provides for data mining of tools for comparative genome databases that integrate data annotations and sequences. Common chromosome from many sources. A common, ongoing task for research that uses genome maps identify major synteny among species. databases is to compare an organism’s genome and proteome Potential gain and loss of genes is suggested by with related organisms, and other sequence datasets (ESTs, Gene Ontology groupings for genes of the new SNPs, transposable elements). This task requires significant species. Summaries of essential genome statistics computational infrastructure, one where reusable tools, proto- include sizes, genes found and predicted, homology cols and resources will be valuable and significantly reduce among genomes, phylogenetic trees of species duplicative infrastructure and maintenance effort. Software and comparisons of several gene predictions for tools to fully assembly, analyze and compare these genomes sensitivity and specificity in finding new and known are available to bioscientists. The ability to employ these genes. tools on genome datasets is limited to those with extensive computational resources and engineering talent. Effective use of shared cyberinfrastructure in bioinformatics is a prob- lem today. Cluster and Grid computing in bioinformatics INTRODUCTION have followed other disciplines in parallelizing applications, Many new genomes are becoming available this decade. but this is costly and limited to a subset of bioinformatics Current contents of public genome archives exceed 1 billion applications. This database enables bioscientists to have sequence traces from >1000 organisms [http://www.ncbi.nlm. usable access to new genomes shortly after sequencing cen- nih.gov/Web/Newsltr/V15N1/trace.html; (1)]. This number ters make them available, facilitating new science discoveries will increase rapidly as costs drop and scientific uses for and understanding of the evolution, comparative biology and comparing many genomes increases (2). Biologists should genomics of these model organisms. *Tel: +1 812 333 5616; Fax: +1 812 855 6705; Email: [email protected] Ó 2006 The Author(s). This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Research, 2007, Vol. 35, Database issue D481 GENOME INFORMATICS METHODS using 15 methods produced by several contributing groups. The assemblies and predicted genes can be BLASTed, with Common components links to genome maps. BioMart provides searches of the DroSpeGe has been built with common GMOD database full genome annotation sets, allowing selections of genome components and open source software shared with other gen- regions with and without specific features. ome databases. Use of common components facilitates rapid construction and interoperability. The GMOD ARGOS repli- cable genome database template (www.gmod.org/argos/) pro- New species genomes vides a tested set of integrated components. The genome Twelve Drosophila genomes, 10 recently sequenced, contain access tools of GMOD GBrowse [www.gmod.org/gbrowse/; over 2 billion nt, with sizes ranging from a small 133 Mb (3)], BioMart [www.biomart.org; (4)] and BLAST (5) are of D.melanogaster to >230 Mb in Drosophila willistoni available for the Drosophila species genomes. The GMOD (Table 1). The model organism D.melanogaster is approach- Chado relational database schema (www.gmod.org/chado/) ing its fifth major assembly release, and continues to see is used for managing an extensible range of genome informa- significant improvements in genes and genome features. It tion. Middleware in Perl and Java are added to bring together has a known, located complement of 14 000 protein BLAST, BioMart, sequence reports, searches and other bioin- genes. One main impetus for undertaking the sequencing of formatics programs for public access. Another aid to integrat- 11 additional related species is to improve via comparative ing and mining these data is GMOD Lucegene (www.gmod. analyses the knowledge of this major research organism. Downloaded from org/lucegene/), that forms a core component for rapid data Drosophila pseudoobscura, the second related genome, is retrieval by attributes, GBrowse data retrieval and databank in its second major release. The additional species are at partitioning for Grid analyses. DroSpeGe operates on several their first major assembly stage, requiring automated annota- Unix computers; the primary server is a SunFire V20z from tion, quality assessment and cross-species comparisons. Four Sun Microsystems. Genome maps include Drosophila mela- of these new genomes (Dsim, Dsec, Dyak and Dere) are close http://nar.oxfordjournals.org/ nogaster DNA and protein homology, homologies to nine relatives of the model in the melanogaster subgroup. The eukaryote proteomes, marker gene locations, gene predictions remainder range through five other taxonomic groups with Table 1. Drosophila species genomes, abbreviation, sequencing centers and genome size of CAF1 assemblies used at DroSpeGe Abbreviation Species Size (Mb) Sequencing center Dmel Drosophila melanogaster 133 Berkeley Drosophila Genome Project/Celera Dsim Drosophila simulans 142 Genome Sequencing Center, Washington University by guest on November 14, 2015 Dsec Drosophila sechellia 167 Broad Institute Dyak Drosophila yakuba 160 Genome Sequencing Center, Washington University Dere Drosophila erecta 153 Agencourt Bioscience Corporation Dana Drosophila ananassae 231 Agencourt Bioscience Corporation Dper Drosophila persimilis 188 Broad Institute Dpse Drosophila pseudoobscura 153 Human Genome Sequencing Center, Baylor College of Medicine Dwil Drosophila willistoni 237 J. Craig Venter Institute Dmoj Drosophila mojavensis 194 Agencourt Bioscience Corporation Dvir Drosophila virilis 206 Agencourt Bioscience Corporation Dgri Drosophila grimshawi 200 Agencourt Bioscience Corporation Annotations produced by several groups collaboratively are provided for map viewing and data mining. Protein coding gene predictions viewable at this resource include contributions listed in Table 2. Table 2. Drosophila species genome annotations (partial list) included at DroSpeGe, contributed at http://rana.lbl.gov/drosophila/wiki/index.php/ Annotation_Submission Contributor Annotation description S. Batzoglou Lab, Stanford Contrast [http://contra.stanford.edu/contrast/; (6)] predictions M. Brent Lab, Washington University, St Louis N-SCAN [http://mblab.wustl.edu/; 7)] predictions with melanogaster alignments D. Gilbert Lab, Indiana University SNAP [http://www.biomedcentral.com/1471-2105/5/59; (8)] predictions, model organism gene homologies M. Eisen Lab, UC Berkeley/LBNL GeneWise (9), GeneMapper [http://bio.math.berkeley.edu/genemapper/; (10)], Exonerate (11) annotations R. Guigo´ Genome Bioinformatics Lab,
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