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The Relation between Indel Length and Functional Divergence: A Formal Study [chapter]

Raheleh Salari, Alexander Schönhuth, Fereydoun Hormozdiari, Artem Cherkasov, S. Cenk Sahinalp
Lecture Notes in Computer Science  
Distinguishing between indel and non-indel pairs, according to our novel statistics, revealed that, despite having the same sequence identity, indel pairs are significantly less functionally similar than  ...  This suggests that indels cause more severe functional changes than other types of sequence variation and that indel statistics should be taken into additional account to assess functional similarity between  ...  Acknowledgements We would like to greatly thank Francisco Couto and Daniel Faria for computing the GO similarity values and Michael Coons for helpful discussions and proofreading the mathematical parts  ... 
doi:10.1007/978-3-540-87361-7_28 fatcat:5tvggzvgincjtk6s7x3btbuop4

Amplitude spectrum distance: measuring the global shape divergence of protein fragments

Clovis Galiez, François Coste
2015 BMC Bioinformatics  
Defined as the distance between their amplitude spectra, ASD can be computed efficiently and provides a parameter-free measure of the global shape dissimilarity of two fragments.  ...  Yet, there is still a lack of more progressive scores, with meaningful intermediate values, for the comparison, retrieval or clustering of distantly related fragments.  ...  Acknowledgements We gratefully acknowledge Inria for the 3-years PhD grant "Inria Cordi-S" attributed to CG.  ... 
doi:10.1186/s12859-015-0693-y pmid:26268224 pmcid:PMC4535829 fatcat:rtth4iuvl5fupilxs25aqbkudi

Comparative analysis of bacterial genomes: identification of divergent regions in mycobacterial strains using an anchor-based approach

Anchal Vishnoi, Rahul Roy, Alok Bhattacharya
2007 Nucleic Acids Research  
ABWGC was able to correctly pick 1002 additional indels (size >100 nt) between the two organisms in contrast to MUMmer, a popular tool for comparative genomics.  ...  ABWGC was able to identify correctly repeat expansion and indels in a set of simulated sequences.  ...  Bhattacharya and Vivek Thakur for discussion and valuable comments. The authors thank the anonymous referees for valuable suggestions.  ... 
doi:10.1093/nar/gkm209 pmid:17488849 pmcid:PMC1931498 fatcat:iusrd5b3bfhp7euvfhxbdiwdtm

Extraordinary Sequence Divergence at Tsga8, an X-linked Gene Involved in Mouse Spermiogenesis

J. M. Good, D. Vanderpool, K. L. Smith, M. W. Nachman
2010 Molecular biology and evolution  
This population-level variation was coupled with striking divergence in protein sequence and length between closely related mouse species.  ...  We then sequenced five very rapidly evolving genes within and between several closely related species of mice in the genus Mus.  ...  .), the National Institute of Health grant (1 R01 GM074245-01A1, M.W.N.), and start-up research funds from the University of Montana.  ... 
doi:10.1093/molbev/msq348 pmid:21186189 pmcid:PMC3115680 fatcat:rkov7hkcljeh7guk4lj6v4bcrm

Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication

Maojun Wang, Lili Tu, Min Lin, Zhongxu Lin, Pengcheng Wang, Qingyong Yang, Zhengxiu Ye, Chao Shen, Jianying Li, Lin Zhang, Xiaolin Zhou, Xinhui Nie (+12 others)
2017 Nature Genetics  
to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of  ...  X. (2017) 'Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication.', Nature genetics., 49 (4). pp. 579-587.  ...  This reveals large population divergence between the 110 Chinese group and the Wild group.  ... 
doi:10.1038/ng.3807 pmid:28263319 fatcat:uljjhgnidzhxdkvtutwklrtlfe

TwinCons: Conservation score for uncovering deep sequence similarity and divergence

Petar I. Penev, Claudia Alvarez-Carreño, Eric Smith, Anton S. Petrov, Loren Dean Williams, Christos A. Ouzounis
2021 PLoS Computational Biology  
TwinCons detects a strong sequence conservation signal between bacterial and archaeal rProteins related by circular permutation.  ...  The output distinguishes conserved, variable and signature positions. A signature is conserved within groups but differs between groups.  ...  King and Dr. Gene Lamm for helpful discussions. We also thank Dr. Stephen Altschul and Dr. Yi-Kuo Yu for providing the matrix compositional adjustment code.  ... 
doi:10.1371/journal.pcbi.1009541 pmid:34714829 pmcid:PMC8580257 fatcat:sonjb6afgbhrtoqh4ly4l6hxjm

A Simple Statistical Method for Estimating Type-II (Cluster-Specific) Functional Divergence of Protein Sequences

Xun Gu
2006 Molecular biology and evolution  
In this paper, we focus on the issue of how to statistically identify cluster-specific amino acid residues that are related to the functional divergence after gene duplication.  ...  Case studies are presented and indicate that radical cluster-specific residues are responsible for most of inferred type-II functional divergence, whereas conserved cluster-specific residues appear less  ...  Acknowledgments The author is grateful to Jie Liang, Eric Gaucher, and Kent Vander Velden for constructive comments. This work was partially supported by the National Institutes of Health grants.  ... 
doi:10.1093/molbev/msl056 pmid:16864604 fatcat:gi46kpid7bcgtmbty6tkwf632y

A Computational Study of Elongation Factor G (EFG) Duplicated Genes: Diverged Nature Underlying the Innovation on the Same Structural Template

Tõnu Margus, Maido Remm, Tanel Tenson, Olivier Lespinet
2011 PLoS ONE  
The EFG II specific functional changes could be related to changes in the properties of nucleotide binding and hydrolysis and strengthened ionic interactions between EFG II and the ribosome, particularly  ...  Whereas the gene duplication is postulated to be a prominent factor creating functional novelty, the striking divergence between EFG paralogs can be interpreted in terms of innovation in gene function.  ...  Atkinson for helpful discussion of phylogeny and Ü lo Maivä li for critical reading of the manuscript. We thank Phillip Endicott and Djuddah A.J.  ... 
doi:10.1371/journal.pone.0022789 pmid:21829651 pmcid:PMC3150367 fatcat:lfy3i547kjdadjoy3m7mube7uq

Accurate prediction of orthologs in the presence of divergence after duplication [article]

Manuel Lafond, Mona Meghdari Miardan, David Sankoff
2018 bioRxiv   pre-print
Results: We formalize the notion of divergence after duplication, and provide a theoretical basis for the inference of primary and secondary orthologs.  ...  This has important consequences on the prediction of orthology relationships, since two orthologous genes separated by divergence after duplication may differ in both sequence and function.  ...  Thus for each gene tree and each ∈ {1, 2, 8, 50}, we used INDELiBLE to generate a set of extant gene sequences obtained by multiplying the length each divergent edge by .  ... 
doi:10.1101/294405 fatcat:6f7oezawjzbjbdl3esjvirz7f4

Molecular Parallelisms and Divergences Between Human and Canine Mammary Cancer [article]

Xuemei Lu, Sadaf Ambreen, Yali Hou, Li Guanhan, Binbin Zhao, Gang Bao, Yiwen Song, Degui Lin, Dafei Wu
2020 bioRxiv   pre-print
Collectively, these studies suggest a convergence of some genetic changes in mammary cancer between species but also distinctly different paths to tumorigenesis.  ...  To address the mutation accumulation and antagonistic pleiotropy theory, we investigated Ka/Ks value 237 aging-related genes from human and canine, the aging-related genes do not show selection in canine  ...  Further, we reveal divergent indels and 527 DNA copy number profiles, as compare to human breast cancer, canine mammary cancer showing 528 fewer indels and copy number changes. 529 Importantly, we identified  ... 
doi:10.1101/2020.10.01.318188 fatcat:x5xnknurrbdlfkobtlmseen45u

Patterns and tempo of PCSK9 pseudogenizations suggest an ancient divergence in mammalian cholesterol homeostasis mechanisms

Barbara van Asch, Luís Filipe Teixeira da Costa
2021 Genetica  
We found a dramatic difference in the patterns of PCSK9 retention and loss between Euarchontoglires—where there is strong pressure for gene preservation—and Laurasiatheria, where multiple independent events  ...  These results suggest that there is a fundamental difference in the regulation of cholesterol metabolism between Euarchontoglires and Laurasiatheria, which in turn has important implications for the use  ...  without contacting the corresponding author of the paper and/or seeking permission from the original provider of the genetic material.  ... 
doi:10.1007/s10709-021-00113-x pmid:33515402 fatcat:jkn5qgozvrdizahksgbawcieei

Genomic Divergence in Swedish Warmblood Horses Selected for Equestrian Disciplines

Ablondi, Eriksson, Tetu, Sabbioni, Viklund, Mikko
2019 Genes  
This study shows genetic divergence, due to specialization towards different disciplines in SWB horses.  ...  The aim of this study was to explore the genomic structure of SWB horses to evaluate the presence of genomic subpopulations, and to search for signatures of selection in subgroups of SWB with high or low  ...  Data Availability: The datasets in the current study was generated and analyzed in collaboration with the Swedish Warmblood Association and has a commercial value for them.  ... 
doi:10.3390/genes10120976 pmid:31783652 pmcid:PMC6947233 fatcat:hag4jjcjo5eufpybcxo3mqrjw4

Genome-enabled discovery of evolutionary divergence in brains and behavior

Chinar Patil, Jonathan B. Sylvester, Kawther Abdilleh, Michael W. Norsworthy, Karen Pottin, Milan Malinsky, Ryan F. Bloomquist, Zachary V. Johnson, Patrick T. McGrath, Jeffrey T. Streelman
2021 Scientific Reports  
AbstractLake Malawi cichlid fishes exhibit extensive divergence in form and function built from a relatively small number of genetic changes.  ...  We highlight the promise of evolutionary reverse genetics—the inference of phenotypic divergence from unbiased genome sequencing and then empirical validation in natural populations.  ...  Acknowledgements This work was supported by Grants from the NIH (R01GM101095, 2R01DE019637-10 to JTS and F32GM128346-01A1 to ZVJ) and the Human Frontiers Science Program (RGP0052/2019 to JTS).  ... 
doi:10.1038/s41598-021-92385-8 pmid:34155279 fatcat:dtun6fndv5h3detphrrbc5et2i

MicroRNA Sequence Variation Potentially Contributes to Within-Species Functional Divergence in the NematodeCaenorhabditis briggsae

Richard Jovelin, Asher D. Cutter
2011 Genetics  
We find that some mutations suggest functional divergence on the basis of requirements for target site recognition and computational prediction of the effects of the polymorphisms on RNA folding.  ...  In this study, we investigate allelic variation at microRNA loci in the nematode Caenorhabditis briggsae, a close relative of C. elegans.  ...  J. is supported by a postdoctoral fellowship from the Ontario Ministry of Research and Innovation and A.D.C. is supported by the Natural Sciences and Engineering Research Council of Canada and a Canada  ... 
doi:10.1534/genetics.111.132795 pmid:21890738 pmcid:PMC3213355 fatcat:vs67zjvu3zeybi32tqa7b4vut4

Divergent clonal selection dominates medulloblastoma at recurrence

A. Sorana Morrissy, Livia Garzia, David J. H. Shih, Scott Zuyderduyn, Xi Huang, Patryk Skowron, Marc Remke, Florence M. G. Cavalli, Vijay Ramaswamy, Patricia E. Lindsay, Salomeh Jelveh, Laura K. Donovan (+126 others)
2016 Nature  
The development of targeted anti-cancer therapies through the study of cancer genomes is intended to increase survival rates and decrease treatment-related toxicity.  ...  Targeted therapy is unlikely to be effective in the absence of the target, therefore our results offer a simple, proximal, and remediable explanation for the failure of prior clinical trials of targeted  ...  Acknowledgments We would like to thank the Toronto Centre for Phenogenomics for animal housing and veterinary support, and the Preclinical Core II and animal research facility at STTARR (Spatiotemporal  ... 
doi:10.1038/nature16478 pmid:26760213 pmcid:PMC4936195 fatcat:lx2l7h35unfg7helet7mtjcyzi
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