CusProSe: a customizable protein annotation software with an application to the prediction of fungal secondary metabolism genes
Abstract We report here a new application, CustomProteinSearch (CusProSe), whose purpose is to help users to search for proteins of interest based on their domain composition. The application is customizable. It consists of two independent tools, IterHMMBuild and ProSeCDA. IterHMMBuild allows the it...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-01-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-27813-y |
| _version_ | 1811175879158530048 |
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| author | Leonor Oliveira Nicolas Chevrollier Jean-Felix Dallery Richard J. O’Connell Marc-Henri Lebrun Muriel Viaud Olivier Lespinet |
| author_facet | Leonor Oliveira Nicolas Chevrollier Jean-Felix Dallery Richard J. O’Connell Marc-Henri Lebrun Muriel Viaud Olivier Lespinet |
| author_sort | Leonor Oliveira |
| collection | DOAJ |
| description | Abstract We report here a new application, CustomProteinSearch (CusProSe), whose purpose is to help users to search for proteins of interest based on their domain composition. The application is customizable. It consists of two independent tools, IterHMMBuild and ProSeCDA. IterHMMBuild allows the iterative construction of Hidden Markov Model (HMM) profiles for conserved domains of selected protein sequences, while ProSeCDA scans a proteome of interest against an HMM profile database, and annotates identified proteins using user-defined rules. CusProSe was successfully used to identify, in fungal genomes, genes encoding key enzyme families involved in secondary metabolism, such as polyketide synthases (PKS), non-ribosomal peptide synthetases (NRPS), hybrid PKS-NRPS and dimethylallyl tryptophan synthases (DMATS), as well as to characterize distinct terpene synthases (TS) sub-families. The highly configurable characteristics of this application makes it a generic tool, which allows the user to refine the function of predicted proteins, to extend detection to new enzymes families, and may also be applied to biological systems other than fungi and to other proteins than those involved in secondary metabolism. |
| first_indexed | 2024-04-10T19:43:06Z |
| format | Article |
| id | doaj.art-6b5b54ca42974d18b9a31e5969d21caa |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-04-10T19:43:06Z |
| publishDate | 2023-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-6b5b54ca42974d18b9a31e5969d21caa2023-01-29T12:12:08ZengNature PortfolioScientific Reports2045-23222023-01-0113111310.1038/s41598-023-27813-yCusProSe: a customizable protein annotation software with an application to the prediction of fungal secondary metabolism genesLeonor Oliveira0Nicolas Chevrollier1Jean-Felix Dallery2Richard J. O’Connell3Marc-Henri Lebrun4Muriel Viaud5Olivier Lespinet6Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRSInstitute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRSUniversité Paris-Saclay, INRAE, UR BIOGERUniversité Paris-Saclay, INRAE, UR BIOGERUniversité Paris-Saclay, INRAE, UR BIOGERUniversité Paris-Saclay, INRAE, UR BIOGERInstitute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRSAbstract We report here a new application, CustomProteinSearch (CusProSe), whose purpose is to help users to search for proteins of interest based on their domain composition. The application is customizable. It consists of two independent tools, IterHMMBuild and ProSeCDA. IterHMMBuild allows the iterative construction of Hidden Markov Model (HMM) profiles for conserved domains of selected protein sequences, while ProSeCDA scans a proteome of interest against an HMM profile database, and annotates identified proteins using user-defined rules. CusProSe was successfully used to identify, in fungal genomes, genes encoding key enzyme families involved in secondary metabolism, such as polyketide synthases (PKS), non-ribosomal peptide synthetases (NRPS), hybrid PKS-NRPS and dimethylallyl tryptophan synthases (DMATS), as well as to characterize distinct terpene synthases (TS) sub-families. The highly configurable characteristics of this application makes it a generic tool, which allows the user to refine the function of predicted proteins, to extend detection to new enzymes families, and may also be applied to biological systems other than fungi and to other proteins than those involved in secondary metabolism.https://doi.org/10.1038/s41598-023-27813-y |
| spellingShingle | Leonor Oliveira Nicolas Chevrollier Jean-Felix Dallery Richard J. O’Connell Marc-Henri Lebrun Muriel Viaud Olivier Lespinet CusProSe: a customizable protein annotation software with an application to the prediction of fungal secondary metabolism genes Scientific Reports |
| title | CusProSe: a customizable protein annotation software with an application to the prediction of fungal secondary metabolism genes |
| title_full | CusProSe: a customizable protein annotation software with an application to the prediction of fungal secondary metabolism genes |
| title_fullStr | CusProSe: a customizable protein annotation software with an application to the prediction of fungal secondary metabolism genes |
| title_full_unstemmed | CusProSe: a customizable protein annotation software with an application to the prediction of fungal secondary metabolism genes |
| title_short | CusProSe: a customizable protein annotation software with an application to the prediction of fungal secondary metabolism genes |
| title_sort | cusprose a customizable protein annotation software with an application to the prediction of fungal secondary metabolism genes |
| url | https://doi.org/10.1038/s41598-023-27813-y |
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