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Zenodo
2024
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| Online Access: | https://doi.org/10.5281/zenodo.13743267 |
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Table of Contents:
- <p><strong>KEGG functional annotation using KofamScan v1.3.0</strong></p> <p>These tables are larger alternative versions to the KOfam tables included in the North Pacific Eukaryotic Gene Catalog protein data repository here: <a href="../records/12630398">https://zenodo.org/records/12630398</a><br><br>A full description of this data is published in Scientific Data, available here: <a href="https://www.nature.com/articles/s41597-024-04005-5" target="_blank" rel="noopener">The North Pacific Eukaryotic Gene Catalog of metatranscriptome assemblies and annotations</a>. Please cite this publication if your research uses this data:<br><br>Groussman, R. D., Coesel, S. N., Durham, B. P., Schatz, M. J., & Armbrust, E. V. (2024). The North Pacific Eukaryotic Gene Catalog of metatranscriptome assemblies and annotations. <em>Scientific Data</em>, <em>11</em>(1), 1161.<br><br>Clustered protein sequences were annotated against the KEGG collection (release 104.0) of 20,819 protein family Hidden Markov Models (HMMs) using <a href="https://github.com/takaram/kofam_scan" target="_blank" rel="noopener">KofamScan </a>and KofamKOALA. Kofam annotation code is documented in the project github repository here: <a href="https://github.com/armbrustlab/NPac_euk_gene_catalog/blob/main/scripts/aa_data/NPEGC.kofamscan_function.sh">NPEGC.kofamscan_function.sh</a></p> <p>Excerpt of core NPEGC_kofam function:</p> <p><code># Define input FASTA</code><br><code>local INPUT_FASTA="NPac.${STUDY}.bf100.id99.aa.fasta"</code></p> <p><code># KofamScan call</code><br><code>${KOFAM_DIR}/kofam_scan-1.3.0/exec_annotation -f detail-tsv -E ${EVALUE} -o ${ANNOTATION_DIR}/NPac.${STUDY}.bf100.id99.aa.tsv ${FASTA_DIR}/${INPUT_FASTA}</code></p> <p>Unprocessed annotation results were filtered with a minimum score of 30 to remove low-scoring matches:<br><br><code>zcat NPac.<em><u>NPacID</u></em>.kofam.tsv.gz | awk -F'\t' '{ gsub(/"/, "", $5); $5 = $5 + 0; if ($5 >= 30) print }' | gzip > NPac.<em><u>NPacID</u></em>.UW.bf100.id99.aa.incT30.tsv.gz</code></p>