SAPFIR: A webserver for the identification of alternative protein features
Abstract Background Alternative splicing can increase the diversity of gene functions by generating multiple isoforms with different sequences and functions. However, the extent to which splicing events have functional consequences remains unclear and predicting the impact of splicing events on prot...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2022-06-01
|
| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12859-022-04804-w |
| _version_ | 1818547178806706176 |
|---|---|
| author | Delong Zhou Yvan Tran Sherif Abou Elela Michelle S. Scott |
| author_facet | Delong Zhou Yvan Tran Sherif Abou Elela Michelle S. Scott |
| author_sort | Delong Zhou |
| collection | DOAJ |
| description | Abstract Background Alternative splicing can increase the diversity of gene functions by generating multiple isoforms with different sequences and functions. However, the extent to which splicing events have functional consequences remains unclear and predicting the impact of splicing events on protein activity is limited to gene-specific analysis. Results To accelerate the identification of functionally relevant alternative splicing events we created SAPFIR, a predictor of protein features associated with alternative splicing events. This webserver tool uses InterProScan to predict protein features such as functional domains, motifs and sites in the human and mouse genomes and link them to alternative splicing events. Alternative protein features are displayed as functions of the transcripts and splice sites. SAPFIR could be used to analyze proteins generated from a single gene or a group of genes and can directly identify alternative protein features in large sequence data sets. The accuracy and utility of SAPFIR was validated by its ability to rediscover previously validated alternative protein domains. In addition, our de novo analysis of public datasets using SAPFIR indicated that only a small portion of alternative protein domains was conserved between human and mouse, and that in human, genes involved in nervous system process, regulation of DNA-templated transcription and aging are more likely to produce isoforms missing functional domains due to alternative splicing. Conclusion Overall SAPFIR represents a new tool for the rapid identification of functional alternative splicing events and enables the identification of cellular functions affected by a defined splicing program. SAPFIR is freely available at https://bioinfo-scottgroup.med.usherbrooke.ca/sapfir/ , a website implemented in Python, with all major browsers supported. The source code is available at https://github.com/DelongZHOU/SAPFIR . |
| first_indexed | 2024-12-12T08:03:15Z |
| format | Article |
| id | doaj.art-8143bdd440454c0987c3385c5acd3aae |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-12T08:03:15Z |
| publishDate | 2022-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-8143bdd440454c0987c3385c5acd3aae2022-12-22T00:32:04ZengBMCBMC Bioinformatics1471-21052022-06-0123111310.1186/s12859-022-04804-wSAPFIR: A webserver for the identification of alternative protein featuresDelong Zhou0Yvan Tran1Sherif Abou Elela2Michelle S. Scott3Département de Microbiologie et d’infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de SherbrookeDépartement de Biochimie et Génomique Fonctionnelle, Faculté de Médecine et des Sciences de la Santé, Université de SherbrookeDépartement de Microbiologie et d’infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de SherbrookeDépartement de Biochimie et Génomique Fonctionnelle, Faculté de Médecine et des Sciences de la Santé, Université de SherbrookeAbstract Background Alternative splicing can increase the diversity of gene functions by generating multiple isoforms with different sequences and functions. However, the extent to which splicing events have functional consequences remains unclear and predicting the impact of splicing events on protein activity is limited to gene-specific analysis. Results To accelerate the identification of functionally relevant alternative splicing events we created SAPFIR, a predictor of protein features associated with alternative splicing events. This webserver tool uses InterProScan to predict protein features such as functional domains, motifs and sites in the human and mouse genomes and link them to alternative splicing events. Alternative protein features are displayed as functions of the transcripts and splice sites. SAPFIR could be used to analyze proteins generated from a single gene or a group of genes and can directly identify alternative protein features in large sequence data sets. The accuracy and utility of SAPFIR was validated by its ability to rediscover previously validated alternative protein domains. In addition, our de novo analysis of public datasets using SAPFIR indicated that only a small portion of alternative protein domains was conserved between human and mouse, and that in human, genes involved in nervous system process, regulation of DNA-templated transcription and aging are more likely to produce isoforms missing functional domains due to alternative splicing. Conclusion Overall SAPFIR represents a new tool for the rapid identification of functional alternative splicing events and enables the identification of cellular functions affected by a defined splicing program. SAPFIR is freely available at https://bioinfo-scottgroup.med.usherbrooke.ca/sapfir/ , a website implemented in Python, with all major browsers supported. The source code is available at https://github.com/DelongZHOU/SAPFIR .https://doi.org/10.1186/s12859-022-04804-wAlternative splicingProtein functionProtein domainProtein domain conservation |
| spellingShingle | Delong Zhou Yvan Tran Sherif Abou Elela Michelle S. Scott SAPFIR: A webserver for the identification of alternative protein features BMC Bioinformatics Alternative splicing Protein function Protein domain Protein domain conservation |
| title | SAPFIR: A webserver for the identification of alternative protein features |
| title_full | SAPFIR: A webserver for the identification of alternative protein features |
| title_fullStr | SAPFIR: A webserver for the identification of alternative protein features |
| title_full_unstemmed | SAPFIR: A webserver for the identification of alternative protein features |
| title_short | SAPFIR: A webserver for the identification of alternative protein features |
| title_sort | sapfir a webserver for the identification of alternative protein features |
| topic | Alternative splicing Protein function Protein domain Protein domain conservation |
| url | https://doi.org/10.1186/s12859-022-04804-w |
| work_keys_str_mv | AT delongzhou sapfirawebserverfortheidentificationofalternativeproteinfeatures AT yvantran sapfirawebserverfortheidentificationofalternativeproteinfeatures AT sherifabouelela sapfirawebserverfortheidentificationofalternativeproteinfeatures AT michellesscott sapfirawebserverfortheidentificationofalternativeproteinfeatures |