Common Tasks in PATRIC

This page provides an overview with links to User Guides and Tutorials, organized by common tasks in PATRIC.

Contents:

• Common Tasks Using the Web Interface
  • Working with Sequences
    • Assemble a Set of Reads into Contigs
    • Create an Annotated Genome from a set of contigs and Estimate its Quality
    • Extract as Many Complete Genomes as Possible from a Meta-Genomic Sample
    • Annotate a New Genome and Compare it to Similar Genomes in PATRIC
  • Working with Taxonomic Groups
    • Find Representative Genomes for a Taxon
    • Find Genomes in a Taxon with Specific Attributes
  • Working with Genomes
    • Find the Roles Present in a Genome
    • Compare the Proteomes for a Set of Genomes
    • Visually Compare the Protein Families in a Set of Genomes
    • Determine the Evidence of Quality for a Genome
    • Find the Closest N Genomes to a Particular Genome
  • Working with Protein Families
    • List the Features in a Protein Family and the Genomes Containing Them
    • Find the Function of a Protein Family
  • Working with Features
    • Find the Sequence, Protein Translation, and Other Known Attributes of a Gene
    • Find the Upstream Region of a Gene
    • Find All the Genes in the Same Protein Family As A Feature
    • Create an Alignment and the Associated Phylogenetic Tree from a Set of Features
    • Find the Papers Relating to a Specific Feature
• Common Tasks With P3 Scripts
  • Working with Taxonomic Groupings
    • List Roles that are Found in One Species but not Another
    • Compute How Many Genomes we have in a Particular Genus
    • List the Genomes we have in a Particular Genus
    • Compute the Fraction of the Genomes in a Genus that are Resistant to a Particular Drug
  • Working with Genomes
    • Find a Genome from an Accession Number or Project ID
    • Given a Genome ID, Find the Name
    • Find a Gene by Name in a Particular Genome
    • Display the CDS and RNA features for A Genome Sorted by Location on the Chromosome
    • Compute the Upstream Regions for the Protein-Encoding Genes in a Genome
    • Compute the Codon Usage in a Genome
    • Extract a Fasta File of a Genome’s Contigs
    • List the Protein Sequences for the Genes in a Genome
    • Given a List of Genomes, Produce a List of Pairs of Roles that are Implemented by Genes that are Close on the Chromosome, Sorted by Number of Occurrences
    • Extract the Genomes in a List that have GC Content Values Greater Than a Certain Percentage
    • Compute how Close Two Features are on the Chromosome
    • List the Drugs to which a Genome is Resistant
  • Working with Anti-Microbial Drugs
    • Find Genomes that are Resistant to a Particular Drug
  • Working with Protein Families
    • Compute the Average Length of Proteins in A Particular Family
    • List the Genome and Feature ID for Each Feature in a Protein Family
  • Working with Features
    • Find the Global Protein Family Containing a Particular Feature
    • Find the Function a Particular Feature implements
    • Find a Feature from an Alternate Feature ID
    • Given a Feature ID, Find the Amino Acid Sequence
    • Find How many Genomes have an Identical Protein to a Given Feature
    • Given a Feature ID, Find the Features in the Same Protein Family