DOI: 10.6084/m9.figshare.29803892
title: Supplementary Table S7: All Results of Structural Alignment between Selected Rice Gene Group and Human using the Foldseek

description: Results of structural alignment between selected rice gene group (upregulated gene group and downregulated gene group) and the Human proteome using the Foldseek (ver.9-427df8a).UniProt accessions corresponding to the IDs of rice genes selected based on the HN-score were retrieved using the unipressed (ver. 1.3.0) and UniProt Web Application Programming Interface (API) (accessed on 23 May 2025). Macromolecular Crystallographic Information File (mmCIF) files of predicted protein structures corresponding to the UniProt accessions were retrieved using the AlphaFold protein structure database Web API (accessed on 23 May 2025). Structural alignment using Foldseek (ver.9-427df8a) was performed on the collected mmCIF files with all protein structures (approximately 214 million) in UniProt, including TrEMBL, as an index. The alignment methods used were local alignment using the (1) 3D interaction (3Di) + Amino Acid (AA) Goto-Smith-Waterman algorithm and (2) TM-align (Foldseek-TM), which considers more global structural features [26]. From the structural alignment results for all species, the rice-human structural alignment results were extracted, and this group of hit pairs was used in subsequent analyses in this study.【Column Name Description】<br>"From" column: rice (<i>Oryza sativa subsp. japonica</i>) gene ID"HN5": HN-score (gene expression pattern metrics)<br>"UniProt Accession": rice structure prediction accession (UniProt accession)<br>"foldseek hit": human structure prediction accession (UniProt accession)<br><br>Table S7-1: <b>foldseek_output_uniprot_rice_up_9606_modified</b>: Results of structural alignment of rice upregulated gene group and human using Foldseek (3Di + AA Goto-Smith-waterman algorithm)Table S7-2: <b>foldseek_output_uniprot_rice_up_9606_tmalign</b><b>_modified</b>: Results of structural alignment of rice upregulated gene group and human using Foldseek (Foldseek-TM)Table S7-3: <b>foldseek_output_uniprot_rice_down_9606</b><b>_modified</b>: Results of structural alignment of rice downregulated gene group and human using Foldseek (3Di + AA Goto-Smith-waterman algorithm)Table S7-4: <b>foldseek_output_uniprot_rice_down_9606_tmalign</b><b>_modified</b>: Results of structural alignment of rice downregulated gene group and human using Foldseek (Foldseek-TM)<b>List of execution commands (using Common Workflow Language (CWL), the workflow language):</b>Note: You can use files from the following repositories: https://github.com/yonesora56/HS_rice_analysis<b>(1) Index creation using the </b><code><strong>foldseek databases</strong></code><b> command (network access required)</b><code>cwltool --debug ./Tools/02_foldseek_database.cwl --database Alphafold/UniProt --index_dir_name index_uniprot --index_name uniprot --threads 16</code><br><b>(2) Structural alignment using </b><code><strong>foldseek easy-search</strong></code><b> command</b><b>(rice up & 3Di alignment)</b> <code>cwltool --debug ./Tools/11_foldseek_easy_search.cwl ./config/</code><code>202506_foldseek_easy_search/</code><code>foldseek_easysearch_rice_up.yml</code><b>(rice up & Foldseek-TM)</b> <code>cwltool --debug ./Tools/11_foldseek_easy_search.cwl ./config/202506_foldseek_easy_search/foldseek_easysearch_rice_up_tmalign.yml</code><b>(rice down & 3Di alignment) </b><code>cwltool --debug ./Tools/11_foldseek_easy_search.cwl ./config/</code><code>202506_foldseek_easy_search/</code><code>foldseek_easysearch_rice_down.yml</code><b>(rice down & Foldseek-TM) </b><code>cwltool --debug ./Tools/11_foldseek_easy_search.cwl ./config/</code><code>202506_foldseek_easy_search/</code><code>foldseek_easysearch_rice_down_tmalign.yml</code><br>The following Jupyter notebooks were used to extract the structural alignment results with humans from these results (more details: https://github.com/yonesora56/HS_rice_analysis).<b>(rice up & 3Di alignment)</b> notebooks/12_foldseek_result_parse_1_up.ipynb<b>(rice up & Foldseek-TM)</b> notebooks/12_foldseek_result_parse_1_up_tmalign.ipynb<b>(rice down & 3Di alignment)</b> notebooks/12_foldseek_result_parse_1_down.ipynb<b>(rice down & Foldseek-TM)</b> notebooks/12_foldseek_result_parse_1_down_tmalign.ipynb<br>