Common Tasks Using the Web Interface¶

In this tutorial, we will present examples of common tasks and show how to accomplish them using the PATRIC Web Interface. To keep this page manageable, we link to instructions on separate pages.

Working with Sequences¶

Assemble a Set of Reads into Contigs¶

PATRIC provides an assembly service that allows you to choose between multiple assemblers, using either single-read libraries, paired-end reads, or reads stored online in the NCBI Sequence Read Archive. We have an introductory tutorial and a more detailed guide.

Create an Annotated Genome from a set of contigs and Estimate its Quality¶

PATRIC provides an annotation service that constructs a private genome from contigs and produces a quality report. See Genome Annotation for instructions on submitting the contigs, and Analyzing Genome Quality to read the quality report. A sample contigs input file and the resulting job output can be seen here: Annotation Sample. Note that most of the links in the Genome Report will not work because all annotated genomes are private to the annotating user.

Extract as Many Complete Genomes as Possible from a Meta-Genomic Sample¶

The /user_guides/services/metagenome_binning_service provides this function. For a tutorial, see Using the PATRIC Metagenomic Binning Service. Example input files for binning and their results can be found here: Binning Example.

Annotate a New Genome and Compare it to Similar Genomes in PATRIC¶

This combines several of the tasks listed elsewhere on this page. The Comprehensive Genome Analysis service takes either reads or contigs and creates a private genome integrated into the PATRIC database. It also creates a web page describing the genome and places it into a phylogenetic tree. There is a tutorial on how to use this service here. In Comparing Your New Genome to Existing Neighbors we show how to look at the results, find the closest genomes, and compare the protein families.

Working with Taxonomic Groups¶

Find Representative Genomes for a Taxon¶

NCBI identifies Reference and Representative genomes for each clade and species. To these lists, PATRIC adds UniProt reference genomes, and additional genomes selected by manual curation. Because of their high quality, they are a useful subset for doing certain types of analysis.

For the procedure to list the genomes in a taxonomic grouping, see Locating All Genomes for a Taxonomic Group. Instructions for isolating the Reference and Representative genomes are given on the same page under the heading Finding the Representative and Reference Genomes.

Find Genomes in a Taxon with Specific Attributes¶

For the procedure to list the genomes in a taxonomic grouping, see Locating All Genomes for a Taxonomic Group. Instructions for filtering the list are given on the same page under the heading Filtering the Genomes.

Working with Genomes¶

Find the Roles Present in a Genome¶

This is described at Finding the Roles in a Genome.

Compare the Proteomes for a Set of Genomes¶

This is described at Proteome Comparison: Comparing Annotated Proteins Across Genomes..

Visually Compare the Protein Families in a Set of Genomes¶

This is described at Comparing Protein Families Across Individual Genomes and Genome Groups. A description of the output and how to manipulate it can be found here

Determine the Evidence of Quality for a Genome¶

A quality analysis is performed on every private genome created using Genome Annotation. The analysis results are stored in a file called GenomeReport.html in the annotation service output folder. A description of how to read this file is in the tutorial Analyzing Genome Quality.

Find the Closest N Genomes to a Particular Genome¶

Use the Similar Genome Finder. For more information read Similar Genome Finder Service.

Working with Protein Families¶

List the Features in a Protein Family and the Genomes Containing Them¶

This procedure is described in Finding a Protein Family by ID.

Find the Function of a Protein Family¶

First, get a list of the features in the protein family using Finding a Protein Family by ID or Finding a Feature’s Protein Family. Then use the procedure in Finding the Protein Family Function.

Working with Features¶

Find the Sequence, Protein Translation, and Other Known Attributes of a Gene¶

The many attributes of a feature are displayed on the Feature (Gene) Overview Tab.

Find the Upstream Region of a Gene¶

The upstream region can be seen most clearly using the Compare Region Viewer. The upstream region is shown to the left of the red arrow.

Find All the Genes in the Same Protein Family As A Feature¶

This procedure is described in Finding a Feature’s Protein Family.

Create an Alignment and the Associated Phylogenetic Tree from a Set of Features¶

This is described in Creating a Multiple-Sequence Alignment.

Find the Papers Relating to a Specific Feature¶

This information is displayed in the right-hand column of the Feature (Gene) Overview Tab.