Accurate annotation of human protein-coding small open reading frames
نویسندگان
چکیده
منابع مشابه
sORF finder: a program package to identify small open reading frames with high coding potential
SUMMARY sORF finder is a program package for identifying small open reading frames (sORFs) with high-coding potential. This application allows the identification of coding sORFs according to the nucleotide composition bias among coding sequences and the potential functional constraint at the amino acid level through evaluation of synonymous and non-synonymous substitution rates. AVAILABILITY ...
متن کاملsORF finder: a program package to identify small open reading frames (sORFs) with high coding potential
Summary: sORF finder is a program package for identifying small open reading frames (sORFs) with high coding potential. This application allows identification of coding sORFs according to the nucleotide composition bias among coding sequences and the potential functional constraint at the amino acid level through evaluation of synonymous and nonsynonymous substitution rates. Availability: Onlin...
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Small open reading frames (sORFs) and genes for non-coding RNAs are poorly investigated components of most genomes. Our analysis of 1391 ORFs recently annotated in the soybean symbiont Bradyrhizobium japonicum USDA 110 revealed that 78% of them contain less than 80 codons. Twenty-one of these sORFs are conserved in or outside Alphaproteobacteria and most of them are similar to genes found in tr...
متن کاملHow to Deal with Small Open Reading Frames?
Current ’classical’ algorithms recognizing protein coding sequences do not work effectively with sequences of small length. To deal with this problem we have proposed some improvements of the existing gene finders without any assumed arbitrary threshold. Introduced parameters describe position of tested sequences in the ranking of all small Open Reading Frames and short protein coding genes fou...
متن کاملSmall open reading frames: current prediction techniques and future prospect.
Evidence is accumulating that small open reading frames (sORF, <100 codons) play key roles in many important biological processes. Yet, they are generally ignored in gene annotation despite they are far more abundant than the genes with more than 100 codons. Here, we demonstrate that popular homolog search and codon-index techniques perform poorly for small genes relative to that for larger gen...
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ژورنال
عنوان ژورنال: Nature Chemical Biology
سال: 2019
ISSN: 1552-4450,1552-4469
DOI: 10.1038/s41589-019-0425-0