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Zenodo
2025
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| Online Access: | https://doi.org/10.5281/zenodo.16778021 |
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| _version_ | 1866902304397983744 |
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| author | Tsai, Cheng-Hung Stajich, Jason |
| author_facet | Tsai, Cheng-Hung Stajich, Jason |
| contents | Dbcanlight is a lightweight rewrite of a widely used CAZyme annotation tool run_dbcan. It uses pyhmmer, a Cython binding to HMMER3, in place of the HMMER3 CLI suite as the backend for search processes, improving multithreading performance. In addition, it removes a limitation in run_dbcan that required manual splitting of large sequence files beforehand. The main program dbcanlight comprises three modules - build, search and conclude. The build module help to download the required databases from dbcan website; the search module searches against protein HMM, substrate HMM or diamond databases and reports the hits separately; and the conclude module gathers all the results made by each module and provides a summary. The output format closely resembles that of run_dbcan, with minor cleanup. For example, run_dbcan may report the same substrate multiple times for a gene matching several profiles with that substrate, whereas dbcanlight reports it only once. Dbcanlight only reimplemented the core features of run_dbcan, that is searching for CAZyme and substrate matches by hmmer/diamond/dbcansub. Submodules like signalP, CGCFinder, etc. are not implemented. |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_16778021 |
| institution | Zenodo |
| language | |
| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Dbcanlight: a lightweight CAZyme annotation tool Tsai, Cheng-Hung Stajich, Jason Genomics Functional annotation CAZyme Dbcanlight is a lightweight rewrite of a widely used CAZyme annotation tool run_dbcan. It uses pyhmmer, a Cython binding to HMMER3, in place of the HMMER3 CLI suite as the backend for search processes, improving multithreading performance. In addition, it removes a limitation in run_dbcan that required manual splitting of large sequence files beforehand. The main program dbcanlight comprises three modules - build, search and conclude. The build module help to download the required databases from dbcan website; the search module searches against protein HMM, substrate HMM or diamond databases and reports the hits separately; and the conclude module gathers all the results made by each module and provides a summary. The output format closely resembles that of run_dbcan, with minor cleanup. For example, run_dbcan may report the same substrate multiple times for a gene matching several profiles with that substrate, whereas dbcanlight reports it only once. Dbcanlight only reimplemented the core features of run_dbcan, that is searching for CAZyme and substrate matches by hmmer/diamond/dbcansub. Submodules like signalP, CGCFinder, etc. are not implemented. |
| title | Dbcanlight: a lightweight CAZyme annotation tool |
| topic | Genomics Functional annotation CAZyme |
| url | https://doi.org/10.5281/zenodo.16778021 |