JBPC Generic Model Organism Database Servers

(return to the JBPC Computing home page)

Access to some GMOD/GBrowse resources and databases is firewall or password protected - contact biocomp@lists.mbl.edu for details.


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 biocomp@lists.mbl.edu.


Features

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


JBPC Protist EST Projects

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 biocomp@lists.mbl.edu.



All Other Projects

Project
Description
Access
Investigator

AntonosporaDB

Website for the Antonospora locustae genome project.
Public
Hilary Morrison

Aureococcus

The Aureococcus Serial Analysis of Gene Expression (SAGE) project. Genome and EST data acquired from GenBank and other external sources.
Private
Sonya Dyhrman

Blochmannia pennsylvanicus

The genome sequence of Blochmannia pennsylvanicus (GenBank CP000016), with addition of Serial Analysis of Gene Expression data.
Private
Jennifer Wernegreen, Andrew McArthur

Brachionus manjavacas cDNA

The Brachionus manjavacas RUS cDNA library assembly and annotation database (version 4).
Public
David Mark Welch

Brachionus manjavacas EST

The Brachionus manjavacas EST BLASTable database. For comparative blasting purposes only, the GBrowse assembly is not currently available.
Private
David Mark Welch

Brachionus plicatilis mixed EST

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.
Public
David Mark Welch

Brachionus plicatilis male EST

The Brachionus plicatilis NH1L male, normalized EST library assembly and annotation database.
Private
David Mark Welch

Brachionus plicatilis amictic EST

The Brachionus plicatilis NH1L amictic female, normalized EST library assembly and annotation database.
Private
David Mark Welch

Combined Brachionus sp cDNA

The Combined Brachionus sp. cDNA library assembly and annotation database including data from B.plicatilis and B.manjavacas.
Private
David Mark Welch

Emiliania huxleyi

The Emiliania huxleyi Serial Analysis of Gene Expression (SAGE) project. Genome and EST data acquired from GenBank and other external sources.
Public
Sonya Dyhrman, Andrew McArthur

Enterocytozoon bieneusi

The Enterocytozoon ebieneusi Whole genome shotgun sequencing of E. bieneusi
Private
Hilary Morrison

Environmental Sampling Site 396, Fosmids_6_ 56

Fosmids 6 and 56 are genetic sequences from unknown organisms collected at the hydrothermal vent sampling site 396
Private
Julie Huber

Environmental Sampling Site 396, Fosmid 68

Fosmid 68 is a genetic sequence from an unknown organism collected at the hydrothermal vent sampling site 396
Private
Julie Huber

Environmental Sampling Site 396, Fosmid 87

Fosmid 87 is a genetic sequence from an unknown organism collected at the hydrothermal vent sampling site 396
Private
Julie Huber

Fosmid 20J22

Fosmid 20J22 assembly of a test fosmid using capillary, GS20 and FLX data
Private
David Mark Welch

GiardiaDB
(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
Private
Giardia Contact Form

Marinobacter aquaeolei
(complete genome)

Annotation of the complete Marinobacter aquaeolei genome, using genome data acquired from the DOE Joint Genome Institute.
Private
Susan Huse

Philodina roseola

Sequence assembly and automated annotation of cosmid and other sequences of the rotifer Philodina roseola.
Private
David Mark Welch

Philodina roseola cDNA

Normalized cDNA library for Philodina roseola (PrA library).
Private
David Mark Welch

Schistosoma mansoni EST

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.
Private
Andrew McArthur

Synechococcus
4320_2, RS9916, CC9605, CC9902, RS9917, WH5701, WH7805

Annotation of Synechococcus genome assemblies.
Private
Anton Post