Batch Cloning Gene List

Design gene-deletion clones for Schizosaccharomyces pombe in batch.

How to use

Enter S. pombe systematic gene IDs (e.g. SPBC15D4.01c).
Select a marker plasmid.
Specify verification primers (optional).
The pipeline fetches cloning primers from the Pombe Primer Project (PPPP).
Designs homologous-recombination strategies for each gene.

What it returns

After a delay (can be long), it returns a ZIP archive with:

Per-gene folders that contain:
- Genbank files with the sequences involved
- A json file containing the entire cloning strategy. You can drag-and-drop it into the OpenCloning website to visualize the strategy. It will look similar to this.
Summary tables (TSV, Excel, YAML)

Best way to get started

Just try with the below example, it will return a zip file and you can drag-and-drop the json file into OpenCloning to visualize the strategy. Check also the summary.xlsx file to see the primers.

Gene list (one gene per line):

S. pombe systematic IDs only (e.g. SPAPB1A10.09, SPBC15D4.01c). One gene ID per line; empty lines are ignored.

Plasmid source

The plasmid supplies the marker cassette (e.g. KanMX6, NatMX6) to be PCR-amplified and integrated into each gene locus via homologous recombination.

Provide Addgene Identifier
Upload Plasmid File

Addgene identifier

Numeric Addgene ID of the plasmid (e.g. 19343 for pFA6a-KanMX6). Find IDs at addgene.org.

Checking primers

Primers used for PCR verification of marker cassette integration. Choose NatMX6 or KanMX6 for standard cassettes, or "Other" to enter custom primers (e.g. for HygMX6 or another marker).

NatMx6
KanMx6
Other

Checking primer (forward)

Aligns to the top strand of the modified allele and pairs with a right-side primer. DNA bases only (A, C, G, T).

Checking primer (reverse)

Aligns to the bottom strand of the modified allele and pairs with a left-side primer. DNA bases only (A, C, G, T).

Submit to run the pipeline. You will receive a ZIP file containing per-gene folders (primers, cloning strategy, GenBank sequences) and summary tables (TSV, Excel, YAML).