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Method: Three-dimensional missense tolerance ratio analysis
- Riley E. Perszyk,
- Anders S. Kristensen,
- Polina Lyuboslavsky,
- and Stephen F. Traynelis
Genome Res. August 2021 31: 1447-1461; Published in Advance July 22, 2021, doi:10.1101/gr.275528.121
...signatures about the protein structure-function relationships and provide an unbiased view of various protein functions in the context of human health. This information can be used to determine regional intolerance to variation, defined as the missense tolerance ratio (MTR), which is an indicator...
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Resource: The fine-scale recombination rate variation and associations with genomic features in a butterfly
- Aleix Palahí i Torres,
- Lars Höök,
- Karin Näsvall,
- Daria Shipilina,
- Christer Wiklund,
- Roger Vila,
- Peter Pruisscher,
- and Niclas Backström
Genome Res. May 2023 33: 810-823; Published in Advance June 12, 2023, doi:10.1101/gr.277414.122
...sex-ratio). Our results do not support such an effect because no significant difference in recombination rate was observed between autosomes and the Z Chromosomes.A clearly deviating recombination rate was found for Chromosome 16 (15.3 cM/Mb), and that explains why the association between chromosome...
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Research: Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks
- Marta Farré,
- Jaebum Kim,
- Anastasia A. Proskuryakova,
- Yang Zhang,
- Anastasia I. Kulemzina,
- Qiye Li,
- Yang Zhou,
- Yingqi Xiong,
- Jennifer L. Johnson,
- Polina L. Perelman,
- Warren E. Johnson,
- Wesley C. Warren,
- Anna V. Kukekova,
- Guojie Zhang,
- Stephen J. O'Brien,
- Oliver A. Ryder,
- Alexander S. Graphodatsky,
- Jian Ma,
- Harris A. Lewin,
- and Denis M. Larkin
Genome Res. April 2019 29: 576-589; Published in Advance February 13, 2019, doi:10.1101/gr.239863.118
...bovidae ancestral chromosomes (Table 1; Supplemental Table S3).Evolutionary breakpoint regions and multispecies homologous synteny blocksWe identified and classified genomic intervals that flank EBRs as well as mammalian msHSBs found in the cattle . Pairwise HSBs were defined at 300-kbp resolution...
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Method: Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes
- Michael F. Lin,
- Pouya Kheradpour,
- Stefan Washietl,
- Brian J. Parker,
- Jakob S. Pedersen,
- and Manolis Kellis
Genome Res. November 2011 21: 1916-1928; Published in Advance October 12, 2011, doi:10.1101/gr.108753.110
...the goodness-of-fit of statistical phylogenetic models. Specifically, we can perform a likelihood ratio test (LRT) to assess precisely whether a small estimate of ls explains an observed alignment window better than the average rates assumed by the Figure 1. (A) Examples of local synonymous rate variation...
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12 Drosophila Genomes/Letter: Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes
- Michael F. Lin,
- Joseph W. Carlson,
- Madeline A. Crosby,
- Beverley B. Matthews,
- Charles Yu,
- Soo Park,
- Kenneth H. Wan,
- Andrew J. Schroeder,
- L. Sian Gramates,
- Susan E. St. Pierre,
- Margaret Roark,
- Kenneth L. Wiley, Jr.,
- Rob J. Kulathinal,
- Peili Zhang,
- Kyl V. Myrick,
- Jerry V. Antone,
- Susan E. Celniker,
- William M. Gelbart,
- and Manolis Kellis
Genome Res. December 2007 17: 1823-1836; Published in Advance November 7, 2007, doi:10.1101/gr.6679507
...ratio and d N / d S rate ( Yang and Bielawski 2000 ; Nekrutenko et al. 2002 ), but it is more suitable for -wide gene identification strategies with many informant s. In contrast to methodologies that focus primarily on high sequence conservation to identify candidate genes, the RFC and CSF metrics...
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Method: Comprehensive viral enrichment enables sensitive respiratory virus genomic identification and analysis by next generation sequencing
- Brigid M. O'Flaherty,
- Yan Li,
- Ying Tao,
- Clinton R. Paden,
- Krista Queen,
- Jing Zhang,
- Darrell L. Dinwiddie,
- Stephen M. Gross,
- Gary P. Schroth,
- and Suxiang Tong
Genome Res. June 2018 28: 869-877; Published in Advance April 27, 2018, doi:10.1101/gr.226316.117
...reference virus had a viral Ct higher than 25). To evaluate the relative sensitivity of enrichment, reference virus NAs were first serially diluted (1:10), then mixed with a constant amount of A549 RNA (samples were prepared using a 1:1 ratio by volume). NAs extracted from clinical specimens were either...
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Methods: Uncertainty in homology inferences: Assessing and improving genomic sequence alignment
- Gerton Lunter,
- Andrea Rocco,
- Naila Mimouni,
- Andreas Heger,
- Alexandre Caldeira,
- and Jotun Hein
Genome Res. February 2008 18: 298-309; Published in Advance December 11, 2007, doi:10.1101/gr.6725608
...(corresponding to an average sequence identity of 0.705), and we used a geometric indel model with substitution/indel rate ratio of γ = 7.5 (see Methods section). These parameters result in sequences that are comparable to sequence at human–mouse divergence (mean sequence identity 69%). The simulated sequences...
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Method: Observation of dually decoded regions of the human genome using ribosome profiling data
- Audrey M. Michel,
- Kingshuk Roy Choudhury,
- Andrew E. Firth,
- Nicholas T. Ingolia,
- John F. Atkins,
- and Pavel V. Baranov
Genome Res. November 2012 22: 2219-2229; Published in Advance May 16, 2012, doi:10.1101/gr.133249.111
...of corresponding genomic regions. The regions that are translated in alternative frames are expected to evolve under purifying selection with the ratio of nonsynonymous to synonymous substitutions being significantly below 1 for the amino acid sequences encoded in alternative frames. Also the regions of dual...
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Review: Population genetic inference from genomic sequence variation
- John E. Pool,
- Ines Hellmann,
- Jeffrey D. Jensen,
- and Rasmus Nielsen
Genome Res. March 2010 20: 291-300; Published in Advance January 12, 2010, doi:10.1101/gr.079509.108
...,000 regions of length 1 Mb. Ascertainment correction was made using the two-dimensional frequency spectrum (for both populations together), by retaining variable sites from the simulated data with a probability equal to the ratio of the per-base-pair frequencies of the 2D frequency class between the Hap...
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LETTER: Reconstructing large regions of an ancestral mammalian genome in silico
- Mathieu Blanchette,
- Eric D. Green,
- Webb Miller,
- and David Haussler
Genome Res. December 2004 14: 2412-2423; doi:10.1101/gr.2800104
...acid level for the reconstruction of the ancestral CFTR protein. This corresponds to an ∼99.5% accuracy at the base level, because roughly 2/3 of random base changes are nonsynonymous, and there is a 3:1 ratio of bases to amino acids. This is not as good as the 99.8% accuracy expected, based...

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