Browsing the AAV Atlas

The AAV Atlas provides a comprehensive collection of adeno-associated virus (AAV) sequences and associated metadata. This guide walks through the basic steps of browsing the sequence table within the AAV Atlas database using the GLUE command line interface (CLI).

Accessing the Sequence Table

To view the sequence data stored in the AAV Atlas, use the following command:

list sequence sequenceID species serotype patent_related gb_ref_title gb_ref_journal

This command retrieves and displays the sequence table, presenting key fields such as:

• sequenceID -- Unique identifier for each sequence.

• species -- Species classification of the AAV.

• serotype -- AAV serotype (e.g., AAV1, AAV2, etc.).

• patent_related -- Indicates whether the sequence is linked to a patent (true/false).

• gb_ref_title -- Title of the GenBank reference associated with the sequence.

• gb_ref_journal -- Journal or patent source for the reference.

Example Output

+============+==============+==========+================+=======================================================+========================================================+
| sequenceID |   species    | serotype | patent_related |                     gb_ref_title                      |                     gb_ref_journal                     |
+============+==============+==========+================+=======================================================+========================================================+
| AF028705   | Primate1     | AAV3     | -              |Infectious clones and vectors derived from aden...     |J. Virol. 72 (1), 309-319 (1998)                        |
| AX135805   | Primate1     | AAV2     | true           |Repo-associated virus aav rep78 major regulator...     |WO0132711-A2 5 10-MAY-2001 THE BOARD OF TRUSTEE...      |
| AX282480   | Primate1     | AAV2     | true           |Production of chimeric capsid vectors                  |WO0168888-A2 1 20-SEP-2001 Neurologix, Inc. (US)        |
+============+==============+==========+================+=======================================================+========================================================+

The table displays relevant metadata for each AAV sequence, including associated patents and publications.

Viewing Available Fields

To explore additional sequence table fields that can be included in the output, use tab completion or run the following command:

list sequence [TAB]

This will prompt a list of available fields such as:

collection_month       collection_month_day   collection_year        country               format
full_name                gb_create_date         gb_ref_doi             gb_update_date         isolate               isolation_source
length                   molecule_type          place_sampled          pubmed_id              sampled_host_sci_name source.name
variation_present

You can modify the list sequence command to include any combination of these fields to tailor the output to your needs.

Example (Including Collection Year and Isolate ID)

Here the -s option is used to sort the results by isolate (in reverse order).

list sequence sequenceID species serotype collection_year isolate -s -isolate

Example Output

+============+==============+==========+=================+======================================+
| sequenceID |   species    | serotype | collection_year |               isolate                |
+============+==============+==========+=================+======================================+
| OQ130187   | Primate1     | -        | 2019            | UNMC-p-AAV2-HAdVC108v                |
| MW334987   | Primate1     | -        | 2015            | tk06-par-02                          |
| MW334988   | Primate1     | -        | 2015            | tk06-par-01                          |
| MW334986   | Mammalian1   | CAAV     | 2015            | tk01-par-02                          |
| MN765179   | Primate1     | -        | 2015            | SAfia-849D                           |
| MN765180   | Primate1     | -        | 2015            | SAfia-839D                           |
| MN765184   | Primate1     | -        | 2015            | SAfia-646D                           |
+============+==============+==========+=================+======================================+

Filtering and Sorting by Patent Source (VOYAGER)

To filter sequences based on specific text in the gb_ref_journal field and sort by the creation date, use the following command:

list sequence sequenceID species serotype patent_related gb_create_date gb_ref_title gb_ref_journal -w "gb_ref_journal like '%VOYAGER%'" -s -gb_create_date

Example Output

+============+============+==========+================+================+==============================================================+==============================================================+
| sequenceID |  species   | serotype | patent_related | gb_create_date |                         gb_ref_title                         |                        gb_ref_journal                        |
+============+============+==========+================+================+==============================================================+==============================================================+
| PA917462   | Primate1   | AAV1     | true           | 25-Jul-2024    |COMPOSITIONS AND METHODS OF TREATING HUNTINGTON...            | JP2019519219-A 369 11-JUL-2019 VOYAGER THERAPE...            |
| PA917463   | Primate1   | AAV8     | true           | 25-Jul-2024    |COMPOSITIONS AND METHODS OF TREATING HUNTINGTON...            | JP2019519219-A 370 11-JUL-2019 VOYAGER THERAPE...            |
| PA917468   | Primate1   | AAV2     | true           | 25-Jul-2024    |COMPOSITIONS AND METHODS OF TREATING HUNTINGTON...            | JP2019519219-A 375 11-JUL-2019 VOYAGER THERAPE...            |
+============+============+==========+================+================+==============================================================+==============================================================+

Paginated Output

The output may be paginated, displaying a subset of sequences at a time. Navigate using the following commands:

• N -- Next page

• P -- Previous page

• F -- First page

• L -- Last page

• Q -- Quit pagination

Filtering Results

You can filter the sequence table by specifying conditions within the where clause. For example:

list sequence sequenceID species serotype where "serotype = 'AAV2'"

This filters and displays only sequences with the serotype AAV2.

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For more information on the GLUE core schema, which defines the structure of tables like the sequence table, visit the GLUE Core Schema Documentation.

By following these steps, users can efficiently browse, filter, and explore the extensive sequence data contained in the AAV Atlas.

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