PIRSitePredict for protein functional site prediction using position-specific rules
| Autor: | John S. Garavelli, Hongzhan Huang, Cathy H. Wu, Chuming Chen, Qinghua Wang, Cecilia N. Arighi, C. R. Vinayaka, Darren A. Natale |
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| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
Embryo
Nonmammalian Java Computational biology Leucoraja erinacea Genome General Biochemistry Genetics and Molecular Biology 03 medical and health sciences Annotation Animals Amino Acid Sequence Databases Protein 030304 developmental biology computer.programming_language 0303 health sciences biology 030302 biochemistry & molecular biology Fishes Scyliorhinus canicula Molecular Sequence Annotation biology.organism_classification Workflow Original Article UniProt General Agricultural and Biological Sciences Transcriptome computer Software Information Systems |
| Zdroj: | Database: The Journal of Biological Databases and Curation |
| ISSN: | 1758-0463 |
| Popis: | Methods focused on predicting ‘global’ annotations for proteins (such as molecular function, biological process and presence of domains or membership in a family) have reached a relatively mature stage. Methods to provide fine-grained ‘local’ annotation of functional sites (at the level of individual amino acid) are now coming to the forefront, especially in light of the rapid accumulation of genetic variant data. We have developed a computational method and workflow that predicts functional sites within proteins using position-specific conditional template annotation rules (namely PIR Site Rules or PIRSRs for short). Such rules are curated through review of known protein structural and other experimental data by structural biologists and are used to generate high-quality annotations for the UniProt Knowledgebase (UniProtKB) unreviewed section. To share the PIRSR functional site prediction method with the broader scientific community, we have streamlined our workflow and developed a stand-alone Java software package named PIRSitePredict. We demonstrate the use of PIRSitePredict for functional annotation of de novo assembled genome/transcriptome by annotating uncharacterized proteins from Trinity RNA-seq assembly of embryonic transcriptomes of the following three cartilaginous fishes: Leucoraja erinacea (Little Skate), Scyliorhinus canicula (Small-spotted Catshark) and Callorhinchus milii (Elephant Shark). On average about 1200 lines of annotations were predicted for each species. |
| Databáze: | OpenAIRE |
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