PATRIC Website Offers New Annotation Types, Genome Browser, Protein Family Sorter and More¶
Genomes and Annotations¶
The current PATRIC release includes RAST annotations for approximately 1,850 of the 2,000 complete bacterial genomes currently available in PATRIC. RAST (Rapid Annotation using Subsystem Technology, Aziz et al., 2008) is a fully-automated service for annotating bacterial and archaeal genomes. It provides consistent and high quality genome annotations across the whole phylogenetic tree. Using a single annotation system across all bacterial genomes not only improves the consistency of annotations but also limits the noise and discrepancies that are difficult to rule out when multiple annotation systems are used.
This release also allows users to compare annotations from three different sources, including RAST, RefSeq, and legacy BRCs. When available, genomes have annotations from three different sources displayed side-by-side for easy comparison.
All genomes annotations are available through various pages on PATRIC website, including Taxon Overview, Taxonomy, Genome List, Feature Table, Genome Overview. All of these pages are available as tabs, seen directly under the Taxonomy Overview.
PATRIC | Legacy BRC | RefSeq | |
|---|---|---|---|
Number of genomes | 2,135 | 410 | 2,577 |
Number of genomic features | 15,495,850 | 2,324,786 | 16,647,467 |
Website Enhancements¶
Genome Browser¶
PATRIC now offers Ajax-based genome browser implemented using JBrowse (Skinner et al, 2009). Access to the browser, via tabs, is available at both the genome and feature levels. Links to the genome browser are also available from the Genome List and the Feature Table.
The new browser has tracks for genes, CDSs, RNAs and other miscellaneous features. The browser also allows users to compare the three annotation systems (RefSeq, PATRIC/RAST and Legacy BRC) simultaneously. Each is available by a separate track, allowing the user to do a comparative analysis.
Protein Family Sorter¶
The current PATRIC release provides functional protein families. The families are created using FIGfams, generated from RAST annotations, and allow the user to look at protein conservation among diverse bacterial orders.
Protein Family Sorter allows the users to include or exclude genomes, and also to put genomes into a “don’t care” category, offering more diversity in sorting ability. Users can also filter by family description or FIGfam number.
Information on all families, or on individual members of a specific family, is available by download to either excel or text.
Multiple sequence alignments are generated when requested. They open in a new window.
Metabolic Pathways¶
PATRIC now offers metabolic pathways using KEGG pathway maps. EC numbers that are annotated by RefSeq, PATRIC/RAST or the legacy BRCs are mapped to KEGG pathways. The user can see which annotation system has identified a specific EC on any pathway map allowing a comparative approach.
Pathways are available at both genome and feature levels.
Phylogenetic Trees¶
In this release PATRIC provides Order-level phylogenetic trees for all pathogenic bacteria. These trees show members of the order, and also show details of the parts of the tree that contain the pathogenic genera, which are highlighted in red.
Searches and Tools¶
A new Pathway Search allows user to search pathway data using EC numbers, pathway IDs, or pathway names. Search can be narrowed to a group of genomes using the taxonomy tree, or can be open to all bacteria. Users can also filter by annotation source (RefSeq, PATRIC/RAST, legacy BRCs, or all).
An improved BLAST Search now provides analysis by all flavors (blastn, blastp, blastx, tblastn, tblastx) against the genes and protein sequences from RefSeq, PATRIC/RAST and the legacy BRC annotations. BLAST can also be performed against genome sequences.