Data Sheet 1_AlgaeOrtho, a bioinformatics tool for processing ortholog inference results in algae.docx
Introduction<p>Microalgae constitute a prominent feedstock for producing biofuels and biochemicals by virtue of their prolific reproduction, high bioproduct accumulation, and the ability to grow in brackish and saline water. However, naturally occurring wild type algal strains are rarely optim...
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2025
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| _version_ | 1852022338289139712 |
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| author | Mary-Francis LaPorte (20821568) |
| author2 | Neha Arora (1693135) Struan Clark (18706753) Ambarish Nag (180001) |
| author2_role | author author author |
| author_facet | Mary-Francis LaPorte (20821568) Neha Arora (1693135) Struan Clark (18706753) Ambarish Nag (180001) |
| author_role | author |
| dc.creator.none.fl_str_mv | Mary-Francis LaPorte (20821568) Neha Arora (1693135) Struan Clark (18706753) Ambarish Nag (180001) |
| dc.date.none.fl_str_mv | 2025-03-04T05:17:04Z |
| dc.identifier.none.fl_str_mv | 10.3389/fmicb.2025.1541898.s001 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/dataset/Data_Sheet_1_AlgaeOrtho_a_bioinformatics_tool_for_processing_ortholog_inference_results_in_algae_docx/28530071 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Microbiology bioengineering algae metabolic engineering bioinformatics nutraceuticals protein orthology |
| dc.title.none.fl_str_mv | Data Sheet 1_AlgaeOrtho, a bioinformatics tool for processing ortholog inference results in algae.docx |
| dc.type.none.fl_str_mv | Dataset info:eu-repo/semantics/publishedVersion dataset |
| description | Introduction<p>Microalgae constitute a prominent feedstock for producing biofuels and biochemicals by virtue of their prolific reproduction, high bioproduct accumulation, and the ability to grow in brackish and saline water. However, naturally occurring wild type algal strains are rarely optimal for industrial use; therefore, bioengineering of algae is necessary to generate superior performing strains that can address production challenges in industrial settings, particularly the bioenergy and bioproduct sectors. One of the crucial steps in this process is deciding on a bioengineering target: namely, which gene/protein to differentially express. These targets are often orthologs which are defined as genes/proteins originating from a common ancestor in divergent species. Although bioinformatics tools for the identification of protein orthologs already exist, processing the output from such tools is nontrivial, especially for a researcher with little or no bioinformatics experience.</p>Methods<p>The present study introduces AlgaeOrtho, a user-friendly tool that builds upon the SonicParanoid orthology inference tool (based on an algorithm that identifies potential protein orthologs based on amino acid sequences) and the PhycoCosm database from JGI (Joint Genome Institute) to help researchers identify orthologs of their proteins of interest in multiple diverse algal species.</p>Results<p>The output of this application includes a table of the putative orthologs of their protein of interest, a heatmap showing sequence similarity (%), and an unrooted tree of the putative protein orthologs. Notably, the tool would be instrumental in identifying novel bioengineering targets in different algal strains, including targets in not-fully annotated algal species, since it does not depend on existing protein annotations. We tested AlgaeOrtho using three case studies, for which orthologs of proteins relevant to bioengineering targets, were identified from diverse algal species, demonstrating its ease of use and utility for bioengineering researchers.</p>Discussion<p>This tool is unique in the protein ortholog identification space as it can visualize putative orthologs, as desired by the user, across several algal species.</p> |
| eu_rights_str_mv | openAccess |
| id | Manara_8cc6b9165f75a73cb73fef01ac97483d |
| identifier_str_mv | 10.3389/fmicb.2025.1541898.s001 |
| network_acronym_str | Manara |
| network_name_str | ManaraRepo |
| oai_identifier_str | oai:figshare.com:article/28530071 |
| publishDate | 2025 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | Data Sheet 1_AlgaeOrtho, a bioinformatics tool for processing ortholog inference results in algae.docxMary-Francis LaPorte (20821568)Neha Arora (1693135)Struan Clark (18706753)Ambarish Nag (180001)Microbiologybioengineeringalgaemetabolic engineeringbioinformaticsnutraceuticalsprotein orthologyIntroduction<p>Microalgae constitute a prominent feedstock for producing biofuels and biochemicals by virtue of their prolific reproduction, high bioproduct accumulation, and the ability to grow in brackish and saline water. However, naturally occurring wild type algal strains are rarely optimal for industrial use; therefore, bioengineering of algae is necessary to generate superior performing strains that can address production challenges in industrial settings, particularly the bioenergy and bioproduct sectors. One of the crucial steps in this process is deciding on a bioengineering target: namely, which gene/protein to differentially express. These targets are often orthologs which are defined as genes/proteins originating from a common ancestor in divergent species. Although bioinformatics tools for the identification of protein orthologs already exist, processing the output from such tools is nontrivial, especially for a researcher with little or no bioinformatics experience.</p>Methods<p>The present study introduces AlgaeOrtho, a user-friendly tool that builds upon the SonicParanoid orthology inference tool (based on an algorithm that identifies potential protein orthologs based on amino acid sequences) and the PhycoCosm database from JGI (Joint Genome Institute) to help researchers identify orthologs of their proteins of interest in multiple diverse algal species.</p>Results<p>The output of this application includes a table of the putative orthologs of their protein of interest, a heatmap showing sequence similarity (%), and an unrooted tree of the putative protein orthologs. Notably, the tool would be instrumental in identifying novel bioengineering targets in different algal strains, including targets in not-fully annotated algal species, since it does not depend on existing protein annotations. We tested AlgaeOrtho using three case studies, for which orthologs of proteins relevant to bioengineering targets, were identified from diverse algal species, demonstrating its ease of use and utility for bioengineering researchers.</p>Discussion<p>This tool is unique in the protein ortholog identification space as it can visualize putative orthologs, as desired by the user, across several algal species.</p>2025-03-04T05:17:04ZDatasetinfo:eu-repo/semantics/publishedVersiondataset10.3389/fmicb.2025.1541898.s001https://figshare.com/articles/dataset/Data_Sheet_1_AlgaeOrtho_a_bioinformatics_tool_for_processing_ortholog_inference_results_in_algae_docx/28530071CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/285300712025-03-04T05:17:04Z |
| spellingShingle | Data Sheet 1_AlgaeOrtho, a bioinformatics tool for processing ortholog inference results in algae.docx Mary-Francis LaPorte (20821568) Microbiology bioengineering algae metabolic engineering bioinformatics nutraceuticals protein orthology |
| status_str | publishedVersion |
| title | Data Sheet 1_AlgaeOrtho, a bioinformatics tool for processing ortholog inference results in algae.docx |
| title_full | Data Sheet 1_AlgaeOrtho, a bioinformatics tool for processing ortholog inference results in algae.docx |
| title_fullStr | Data Sheet 1_AlgaeOrtho, a bioinformatics tool for processing ortholog inference results in algae.docx |
| title_full_unstemmed | Data Sheet 1_AlgaeOrtho, a bioinformatics tool for processing ortholog inference results in algae.docx |
| title_short | Data Sheet 1_AlgaeOrtho, a bioinformatics tool for processing ortholog inference results in algae.docx |
| title_sort | Data Sheet 1_AlgaeOrtho, a bioinformatics tool for processing ortholog inference results in algae.docx |
| topic | Microbiology bioengineering algae metabolic engineering bioinformatics nutraceuticals protein orthology |