GMOD.MBL.EDU is our cluster of Advanced Genome Browsers, used for creating online resources for combining and analyzing genome, gene expression, and annotation data for genome-scale sequence data. It is the primary bioinformatics engine for the third phase of the GiardiaDB project, by incorporating genome assembly, genome annotation, gene expression, and high-throughput phylogenetic information into the Generic Model Organism Database (GMOD) paradigm. The GMOD server can be used to support any ongoing genome-level analysis in the JBPC and is currently being used for Antonospora, Blochmania, Trypanosoma, EST, rotifer, and many other projects.
Questions, requests, training help, and bug reports should be emailed to firstname.lastname@example.org.
Add your own genome sequencing data to GMOD. GMOD can support Arachne, TIGR, and PHRAP assemblies and CONSED assembly editing results as part of our collaboration with the AMOS Project. We have a suite of assembly analysis tools allowing assessment of read coverage, scaffolding, and closure predictions.
Our GMOD servers can integrate Serial Analysis of Gene Expression (SAGE) and Massively Parallel Signature Sequencing (MPSS) results with partial genomes, complete genomes, or EST sequences. Advanced gene expression analysis tools are included.
Your annotations and genome features (ORFs, ESTs, tRNAs, repeats, etc) can be mapped to your genome sequences. The General Feature Format is preferred, as are the Gene Ontology Evidence Codes. Alternatively, you can use our genome annotation pipeline to predict protein and functional RNA encoding genes, repeats, assembly mapping, plus functional annotation of predicted proteins (InterPro domains, signal peptides, transmembrane domains, etc.).
Perform complex queries by direct access to your data using SQL. Suggested SQL clients are DBTools (Windows) and sequel-pro (Mac OSX).
GBrowse is the advanced web-based graphical genome browser used by our GMOD projects. You can easily customize the appearance of your data and perform a number of types of searches from within GBrowse. To get started, view the GBrowse General Help (GiardiaDB version).
For a pdf describing all of the various features of the databases, click here
For a pdf detailing how to perform cluster analysis of SAGE data, click here
For a pdf detailing raw SAGE data processing in preparation for import to GMOD, click here
A large number of protist EST sequencing projects are underway at the JBPC. Currently, each set of EST data can be accessed separately but expect a meta-server for comparing shared EST-encoded homologs among organisms soon.
The EST data are currently Private. The lead investigator is Hilary Morrison. Please email any questions about these data to email@example.com.
|Website for the Antonospora locustae genome project.|
|The Aureococcus Serial Analysis of Gene Expression (SAGE) project. Genome and EST data acquired from GenBank and other external sources.|
|The genome sequence of Blochmannia pennsylvanicus (GenBank CP000016), with addition of Serial Analysis of Gene Expression data.|
|The Brachionus manjavacas RUS cDNA library assembly and annotation database (version 4).|
|The Brachionus manjavacas EST BLASTable database. For comparative blasting purposes only, the GBrowse assembly is not currently available.|
|The Brachionus plicatilis NH1L mixed population, unnormalized EST library assembly and annotation database described in Suga et al. 2007. PLoS ONE 2(8): e671. doi:10.1371/journal.pone.0000671.|
|The Brachionus plicatilis NH1L male, normalized EST library assembly and annotation database.|
|The Brachionus plicatilis NH1L amictic female, normalized EST library assembly and annotation database.|
|The Combined Brachionus sp. cDNA library assembly and annotation database including data from B.plicatilis and B.manjavacas.|
|The Emiliania huxleyi Serial Analysis of Gene Expression (SAGE) project. Genome and EST data acquired from GenBank and other external sources.|
|The Enterocytozoon ebieneusi Whole genome shotgun sequencing of E. bieneusi|
|Fosmids 6 and 56 are genetic sequences from unknown organisms collected at the hydrothermal vent sampling site 396|
|Fosmid 68 is a genetic sequence from an unknown organism collected at the hydrothermal vent sampling site 396|
|Fosmid 87 is a genetic sequence from an unknown organism collected at the hydrothermal vent sampling site 396|
|Fosmid 20J22 assembly of a test fosmid using capillary, GS20 and FLX data|
(internal use only)
|Internal copy of the Giardia lamblia genome project for JBPC use only.
The public version of GiardiaDB has moved to www.giardiadb.org
at the National Institute of Allergy and Infectious Diseases Bioinformatics Resource Center
|Annotation of the complete Marinobacter aquaeolei genome, using genome data acquired from the DOE Joint Genome Institute.|
|Sequence assembly and automated annotation of cosmid and other sequences of the rotifer Philodina roseola.|
|Normalized cDNA library for Philodina roseola (PrA library).|
|Annotation of Schistosoma mansoni EST data, including mapping of results of Serial Analysis of Gene Expression (SAGE) experiments. EST sequence data acquired from the TIGR and ONSA genome centers.|
4320_2, RS9916, CC9605, CC9902, RS9917, WH5701, WH7805
|Annotation of Synechococcus genome assemblies.|