SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling
| Autor: | Di Hao, Honghong Zhou, Tingrui Song, Huaxia Luo, Shunmin He, Peng Zhang, Yajing Hao, Runsheng Chen, Yu Zheng, Quan Kang, Lili Zhang, Yanyan Li, Xiaomin Chen |
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| Rok vydání: | 2020 |
| Předmět: |
Protein family
Proteins Reproducibility of Results Translation (biology) Molecular Sequence Annotation Computational biology Genome project Biology biology.organism_classification Biochemistry Rats Computational Mathematics Open reading frame Mice Open Reading Frames Eukaryotic translation Drosophila melanogaster Upstream open reading frame Genetics Animals Ribosome profiling Molecular Biology Ribosomes Caenorhabditis elegans |
| Zdroj: | Genomics, proteomicsbioinformatics. 19(4) |
| ISSN: | 2210-3244 |
| Popis: | Small proteins specifically refer to proteins consisting of less than 100 amino acids translated from small open reading frames (sORFs), which were usually missed in previous genome annotation. The significance of small proteins has been revealed in current years, along with the discovery of their diverse functions. However, systematic annotation of small proteins is still insufficient. SmProt was specially developed to provide valuable information on small proteins for scientific community. Here we present the update of SmProt, which emphasizes reliability of translated sORFs, genetic variants in translated sORFs, disease-specific sORF translation events or sequences, and remarkably increased data volume. More components such as non-ATG translation initiation, function, and new sources are also included. SmProt incorporated 638,958 unique small proteins curated from 3,165,229 primary records, which were computationally predicted from 419 ribosome profiling (Ribo-seq) datasets or collected from literature and other sources from 370 cell lines or tissues in 8 species (Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Danio rerio, Saccharomyces cerevisiae, Caenorhabditis elegans, and Escherichia coli). In addition, small protein families identified from human microbiomes were also collected. All datasets in SmProt are free to access, and available for browse, search, and bulk downloads at http://bigdata.ibp.ac.cn/SmProt/ . |
| Databáze: | OpenAIRE |
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