PATRIC June 2015 Release Features Integrated Comparative Analysis Capabilities with User-Supplied Genomes and New Services for Protein-Based Genome Comparison, RNA-Seq Analysis, and Metabolic Modeling
The June Release delivers the second stage of genome assembly, annotation and integrated analysis in PATRIC. It also includes a new Proteome Comparison Service, RNA-Seq Analysis Service, and Metabolic Modeling Service, plus updates to the Private Workspace and other enhancements.
NOTE: You must have a PATRIC user account and be logged-in to use the services and workspace.
Integrated Genome Comparative Analysis Capability
With this release, users can now view their private genome annotated with the PATRIC Genome Annotation Service in the context of all of the public genomes in PATRIC. This includes the ability to use all of the PATRIC genome presentation and comparative tools such as the Genome Browser, Gene Page, Protein Family Sorter, Comparative Pathway Analysis Service, and Global Search. The user’s genome is visible only to the user, and only if they are logged into PATRIC.
Proteome Comparison Service
The Proteome Comparison Service performs protein sequence-based genome comparison using bidirectional blastp. This service allows users to select up to 8 genomes (either public or private) and compare them to a user selected reference genome. The service also allows users to upload an external genome file in FASTA format for an additional comparison. The genome comparison result is displayed as a Circos genome view on the webpage. Both the SVG image and the bidirectional blastp comparison result can be downloaded. The Proteome Comparison Service can be accessed at https://www.patricbrc.org/app/SeqComparison.
Metabolic Modeling Service
With the release of the Metabolic Modeling Service, users can construct their own metabolic model for any genome in PATRIC. The service includes support for model gap-filling, flux balance analysis, essential gene prediction, and export of models in SBML format. The Metabolic Modeling Service leverages capabilities of the ModelSEED (PMID: 20802497) and is available in PATRIC at https://www.patricbrc.org/app/Reconstruct.
RNA-Seq Analysis Service
PATRIC is now providing services for aligning, assembling, and testing differential expression on RNA-Seq data. The new service provides two recipes for processing RNA-Seq data: 1) Rockhopper, based on the popular Rockhopper tool for processing prokaryotic RNA-Seq data; and 2) Tuxedo, based on the tuxedo suite of tools (i.e., Bowtie, Cufflinks, Cuffdiff). The new tool provides SAM/BAM output for alignment, tab delimited files profiling expression levels, and differential expression test results between conditions. Look for more integration of the resulting RNA-Seq analysis data in coming months. The PATRIC RNA-Seq Analysis Service can be accessed at https://www.patricbrc.org/app/Rnaseq.