CONCUR: quick and robust calculation of codon usage from ribosome profiling data
نویسندگان
چکیده
منابع مشابه
Estimating selection on synonymous codon usage from noisy experimental data.
A key goal in molecular evolution is to extract mechanistic insights from signatures of selection. A case study is codon usage, where despite many recent advances and hypotheses, two longstanding problems remain: the relative contribution of selection and mutation in determining codon frequencies and the relative contribution of translational speed and accuracy to selection. The relevant target...
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Individual mRNAs are translated by multiple ribosomes that initiate translation with an interval of a few seconds. The ribosome speed is codon dependent, and ribosome queuing has been suggested to explain specific data for translation of some mRNAs in vivo. By modeling the stochastic translation process as a traffic problem, we here analyze conditions and consequences of collisions and queuing....
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The hypothesis that codon usage regulates gene expression at the level of translation is tested. Codon usage of Escherichia coli and phage lambda is compared by correspondence analysis, and the basis of this hypothesis is examined by connecting codon and tRNA distributions to polypeptide elongation kinetics. Both approaches indicate that if codon usage was random tRNA limitation would only affe...
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χ measure. In statistics, the χ statstic computes how different the distribution of values is from a uniform distribution. Let d = c1 . . . cN be a DNA string in nucleotide alphabet, and let L be the total number of codons in d that are not Methinine or Tryptophan (the number does include the stop codons though). Let a be a k-degenerate amino acid, and let La be the total number of codons codin...
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کاتالیست یک سنتز جدید برای تیواترها توصیف شده است. واکنش الکل ها با آریل، هتروآریل و آلکیل تیو ل ها درحضور 1،3،5- تری آزو- 2،4،6- تری فسفرین-2،2،4،4،6،6 هگزاکلراید ((tapc به عنوان یک کاتالیست موُثر، بازده های خوب تا عالی از تیواترها را حاصل می کند. علاوه براین، واکنش تحت شرایط بدون فلز و بدون حلال پیش می رود، بنابراین یک مکمل جالب برای روش های شناخته شده سنتز تیواترها ارائه می دهد. یک مکانیسم ا...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2020
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/btaa733