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.
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 Genome Annotations.
- By default, tables show 200 rows of data. For rows beyond 200, the numbers on the right side below the table, allowing advancement throughout pages in increments of 200 rows.
- When a row is selected, the information panel (accessible via the Show/Hide icon at the top of the green Action Bar, provides detailed information for that row including links to other PATRIC genome pages and external resources, such as NCBI protein pages, where appropriate. It also provides access to the corresponding nucleotide and amino acid sequences.
- The vertical green Action Bar, located just to the right of the
feature table provides a set of actions that can be performed on the
features selected in the table:
- 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 the selected features in an overview summary or a table containing on only those features.
- View the genomes associated with the selected feature in an overview summary or a table.
- View selected DNA and/or protein sequence data in FASTA format.
- Create a Multiple Sequence Alignment (MSA) analysis on selected features. For more details see the Multiple Sequence Alignment user guide.
- Utilize the ID Mapping Tool on selected features. For more information see ID Mapping user guide.
- View pathways and associated pathway information for your selected genes. For more information see the Comparative Pathway user guide.
- Customize columns shown/hidden in your results table by clicking the small '+' symbol in the upper right corner of the table. Data may be rearranged by dragging entire columns, adjusting individual column width, and sorting by column.
When filtering a feature table based on keyword, PATRIC matches the user-specified keyword term against the the fields in the table and shows only those with matching text.
You can also filter by clicking the filter icon above the table on the right side. It will open a filter panel wherein you can filter on different columns by value, such as Sequence Type (chromosome, contig, plasmid) and Topology (linear, circular).