2026-10-06T19:24:24Z https://api.figshare.com/v2/oai

oai:figshare.com:article/33752671 2026-09-14T19:25:11Z category_24340 category_24184 item_type_3 month_year_09_2026

PAGODA dataset Chenling Xu (10513421) Ziwei Zhong (5983388) Sean Patrick Leonard (23673614) Industrial molecular engineering of nucleic acids and proteins Bioinformatic methods development essential genes overlapping genes dynamic programming sequence design <p dir="ltr">This dataset contains computational design outputs and experimental screening results associated with PAGODA, a method for designing partially overlapping protein-coding sequences. The files link sequence designs and Potts model scores to enrichment measurements and plate-based growth assessments.</p><p dir="ltr">The dataset includes five CSV files:</p><ul><li><b>hisI_purE_enrichment.csv</b> — 200 records for hisI–purE designs, including nucleotide sequences, frame and overlap annotations, gene-specific enrichment measurements, recomputed Potts scores, and insertion, deletion, and substitution counts.</li><li><b>purE_hisI_enrichment.csv</b> — 200 records for the reverse gene order, purE–hisI, with the same design annotations and enrichment measurements.</li><li><b>ilvE_gltA_enrichment.csv</b> — 445 records for ilvE/gltA designs in both gene orders. Includes sequence and library-design information, primers, Potts scores, condition-specific counts and enrichment values across three replicates, and summary enrichment statistics.</li><li><b>purE_hisI_plate.csv</b> — Growth assessments for 24 purE–hisI designs under no supplementation, histidine supplementation, and adenine supplementation at 24 and 96 hours, together with functional classifications.</li><li><b>screen_results.sample.csv</b> — A sample of 99 computational screening records across multiple gene pairs, including designed nucleotide sequences, initial and optimized protein sequences, sequence coordinates, overlap lengths, scores, insertion/deletion annotations, and design parameters.</li><li><b>screen_results.csv</b> — The full result in the same format as the <b>screen_results.sample.csv</b> </li></ul><p dir="ltr">Files are provided in comma-separated format and can be opened using spreadsheet software or standard data-analysis tools. Blank entries indicate values not provided in the files and should not be interpreted as zero. Associated code is available at <a href="https://github.com/BiosecSFA/PAGODA" target="_blank">https://github.com/BiosecSFA/PAGODA</a>.</p> 2026-09-14T19:25:11Z Dataset Dataset 10.6084/m9.figshare.33752671.v1 https://figshare.com/articles/dataset/PAGODA_dataset/33752671 CC BY 4.0