AptBacterialDB User Guide

Basic Search

The basic search allows users to quickly retrieve aptamer records using keywords such as aptamer ID, target, organism, or sequence. Users can select fields to display and access detailed information by clicking on individual entries.

Advanced Search

The advanced search enables users to perform complex queries using multiple fields and logical operators (AND/OR/NOT). It allows refined filtering across different attributes of the database.

Structure based Search

The structure search enables users to search for aptamer records based on their 2D or 3D structural features such as Dot-Bracket notation, Strand notation, Element string and Minimum Free Energy(MFE).

For detailed instructions, refer to the Search Guide available on the search pages.

The browse module allows users to explore the database through categorized views. Each category provides a structured way to access aptamer records.

• Browse by SELEX Method
• Browse by Target
• Browse by Target Organism
• Browse by Affinity Method
• Browse by Modifications
• Browse by Activity Role
• Browse by Year
• Browse by Length

Clicking on any category displays corresponding entries with detailed information and links to related records.

BLASTN Search

The BLASTN tool enables users to perform nucleotide sequence similarity searches against the AptBacterialDB dataset. By submitting a query sequence, users can identify closely related aptamer sequences, evaluate alignment scores, and explore sequence homology. This tool is useful for comparative analysis, validation of sequences, and discovering similar functional aptamers.

GC content Calculator

The GC Content Calculator allows users to analyze the nucleotide composition of aptamer sequences by determining the percentage of guanine (G) and cytosine (C) bases. This information is important for understanding sequence stability, melting temperature, and structural properties of aptamers.

The Knowledge Graph provides an interactive visualization of relationships between antibacterial aptamers, targets, organisms, and activity roles in AptBacterialDB.

• Use the Search box to find aptamer sequences, targets, organisms, or activity roles.
• Click a node to view detailed information, associated database records, and linked entities. For Aptamer details, click on aptamer nodes and go to ABdb_ID details link.
• Select Expand Neighbors to load additional nodes directly connected to the selected node.
• Use the Zoom In, Zoom Out, and Fit Screen controls to navigate large networks.
• Toggle Display Classes to show or hide specific node categories.
• Different node colors represent different entity types including Aptamers, Targets, Organisms, and Activity Roles. For more information about the nodes check out the browse page for Target, Target Orgnaism and Activity Role.

Users can download curated datasets from AptBacterialDB for further analysis.

• Aptamer sequences in FASTA format
• Predicted secondary structure images

These datasets can be used for sequence analysis, structural studies, and other bioinformatics workflows.

The API module provides programmatic access to the database. Users can retrieve data in structured formats for integration into pipelines and external applications.

This section provides cross-referenced entries from AptBacterialDB that are linked to external aptamer databases such as AptaDB, Aptabase, and the UTexas Aptamer Database. It establishes a mapping between AptBacterialDB identifiers and corresponding records in these resources, allowing users to access extended information beyond this database. The page is organized into separate tables based on source databases. Users can click on database names or linked identifiers to directly navigate to external entries for detailed annotations and validation.