Features are defined segments of a genome. Most often features will code for proteins or RNAs, however some correspond to pseudogenes or repeat regions. For a complete list of genomic feature types, please see PATRIC’s Genomic Feature Types.
Feature tables, located under the Feature Table tab on Organism/Genome Landing Pages, contain all of the identified features for all of the genomes in that genus. Tables may be refined to show subsets of features via various user controls described below. Table controls are also described within our YouTube Feature Table Tutorial.
Searching for a Specific Genomic Feature, Such as a Protein Coding Sequence
Feature tables have the following filtering and sorting capabilities that allow for table manipulation and refinement:
- Filter controls, located at the top of feature tables, allow for data filtration via sequence status, feature type, annotation, and keyword. For a description of the various types of annotation available please see Annotation FAQs.
- By default, tables show 20 rows of data. In a field at the bottom of the table, this number can be changed to any value up to 200 and the table can refreshed.
- Click on links within columns to navigate to specific PATRIC genome pages (Genome Name), NCBI nucleotide page for that genome (Accession), and specific PATRIC locus pages (Locus Tag). Note: The Accession column is not shown in the default view.
- Within the table, click on any Genome Browser icon to view an illustration of a specific feature within the context of it’s genome. For more information please see Genome Browser FAQs.
- The Feature Table Toolbar, located in the light blue row just below the Filter controls, can be used to:
- Save selected items to groups within your Workspace by clicking the Add Feature(s) button. To learn more about how to save data for future visits and utilize your personal Workspace see Workspace FAQs.
- View or download selected DNA and/or protein sequence data in FASTA format. The table itself, or selected data within it, are also downloadable in both excel and .txt file formats.
- View pathways and associated pathway information for your selected genes by clicking the Pathway Summary button.
- Conduct Multiple Sequence Alignment analysis on selected items by clicking the Multiple Sequence Alignment button. For more details on this tool see Multiple Sequence Alignment FAQs.
- Utilize the ID Mapping Tool on selected items by clicking the Map IDs button. For more information on this tool see ID Mapping FAQs.
- Customize columns shown/hidden in your results table with the Columns button. Data may be rearranged by dragging entire columns adjusting individual column width. Available Column Names include: Genome Name, Accession, Locus Tag, RefSeq Locus Tag, Gene Symbol, Genome Browser, Annotation, Feature Type, Start, End, Length (NT), Strand, Protein ID, Length (AA), Anticodon, Product Description, and Bound Moiety.
- Access the PATRIC FAQs glossary within PATRIC eNews by clicking on the PATRIC FAQs button.
Filtering by Keyword
When filtering a feature table based on keyword, PATRIC matches the user-specified keyword term against the following fields: Genome Name, Gene Symbol, Product, Locus Tag, Product Description and Protein ID. All resulting features will contain the user-specific keyword in one or more of those fields.