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Locating Regions in a Sequence under Density Constraints

Benjamin A. Burton, Mathias Hiron
2013 SIAM journal on computing (Print)  
Several biological problems require the identification of regions in a sequence where some feature occurs within a target density range: examples including the location of GC-rich regions, identification  ...  For locating the longest such substring, we develop an algorithm that runs in O(n) time, improving upon the previous best-known O(n log n) result.  ...  Examples include maximizing density under a length constraint [11, 12, 19] , finding all substrings under range of density and length constraints [14, 15] , finding the longest substring whose density  ... 
doi:10.1137/110830605 fatcat:gfqfiydabvav7ad5ppzobu5bji

Pervasive Hitchhiking at Coding and Regulatory Sites in Humans

James J. Cai, J. Michael Macpherson, Guy Sella, Dmitri A. Petrov, Gil McVean
2009 PLoS Genetics  
These correlations persist after controlling for the variation in GC content, density of simple repeats, selective constraint, mutation rate, and depth of sequencing coverage.  ...  We find that the levels of neutral polymorphism are lower in the regions of lower recombination and in the regions of higher functional density or divergence.  ...  We measure levels of neutral variation in the sequences that are less likely to be under selective constraint: they are noncoding, located far from exons, and cannot be aligned with distantly related species  ... 
doi:10.1371/journal.pgen.1000336 pmid:19148272 pmcid:PMC2613029 fatcat:eehwwktz6fgenhxxaeswdqh3gm

Genome-wide signals of positive selection in human evolution

D. Enard, P. W. Messer, D. A. Petrov
2014 Genome Research  
The density of mammalian and primate conserved sequences being equal, large regions that are particularly devoid of human-specific nonsynonymous substitutions may still be under stronger constraint.  ...  We first carry out this test in the regions with low density of conserved coding sequences (CCDS density<0.5%) and thus weak effects of BGS.  ... 
doi:10.1101/gr.164822.113 pmid:24619126 pmcid:PMC4032853 fatcat:mkjdwndvujghxjqmvnc3dpqrjm

Twist-DNA: computing base-pair and bubble opening probabilities in genomic superhelical DNA

Daniel Jost
2013 Computer applications in the biosciences : CABIOS  
Based on a self-consistent linearization of a thermodynamic model of superhelical DNA introduced by Benham, we have developed a program that predicts the locations of these regions by efficiently computing  ...  In particular, positions of superhelically destabilized regions correlate with regulatory sites along the genome.  ...  Calugaru for help in software development.  ... 
doi:10.1093/bioinformatics/btt415 pmid:23864732 fatcat:rlrsspifyndnba2kmdwpltqe4e

A Passive Tracking System Based on Geometric Constraints in Adaptive Wireless Sensor Networks

Biao Zhou, Deockhyeon Ahn, Jungpyo Lee, Chao Sun, Sabbir Ahmed, Youngok Kim
2018 Sensors  
In this paper, we propose a passive tracking scheme exploiting both adaptive-networking LOSL webs and geometric constraint methodology for tracking single targets, as well as multiple targets.  ...  Instead of maintaining a fixed LOSL density, the proposed scheme can adaptively adjust the networking level to save energy while guaranteeing tracking accuracy.  ...  R(A, B, · · · , Z) or R(i) means the region represented by the points A, B, · · · , Z or the located region after i-th-triggered LOSL is detected.  ... 
doi:10.3390/s18103276 pmid:30274276 pmcid:PMC6209868 fatcat:ppzoesbxp5dc5l5qabtljtx5t4

Genome-Wide Analysis of Functional and Evolutionary Features of Tele -Enhancers

Di Huang, Ivan Ovcharenko
2014 G3: Genes, Genomes, Genetics  
In this study, we used whole genome enhancer maps and gene expression profiles to establish a large panel of tele-enhancers.  ...  We investigated sequence features of enhancers separated from their target gene by at least one intermediate gene/exon (named tele-enhancers in this study) and enhancers residing inside their target gene  ...  We observed intronic tele-enhancers being under stronger selection constraint than intergenic teleenhancers (Table S6) , which is in accordance with the finding that functional intronic regions are under  ... 
doi:10.1534/g3.114.010447 pmid:24496725 pmcid:PMC4059231 fatcat:tfvh4axsjbgediujykuk22yxny

Adaptive Framework for Multi-Feature Hybrid Object Tracking

Ahmad Khattak, Gulistan Raja, Nadeem Anjum
2018 Applied Sciences  
The first innovation of this research paper is the development of a dynamically adaptive multi-feature framework for MSPF (AMF-MSPF) in which features are ranked by a ranking module and the top features  ...  The proposed AMF-MSPF framework is tested on different video datasets that exhibit challenging constraints.  ...  Object tracking is one such class of algorithms that automatically locates the region of interest, possibly obscured by challenging constraints [1] .  ... 
doi:10.3390/app8112294 fatcat:7p33keb7dbbdvpwhqmmas52wum

Purifying selection shapes the coincident SNP distribution of primate coding sequences

Chia-Ying Chen, Li-Yuan Hung, Chan-Shuo Wu, Trees-Juen Chuang
2016 Scientific Reports  
We find that this discrepancy cannot fully explained by sequence contexts, shared ancestral polymorphisms, SNP density, and recombination rate, and that coSNP O/E in coding sequences is significantly influenced  ...  After rejecting the possible explanations including sequence contexts, shared ancestral polymorphisms, density of single SNPs, and recombination rate, we showed that: (i) the strength of selective constraints  ...  and nonzero-fold degenerate sites in a region under (c) weak and (d) strong selective constraints.  ... 
doi:10.1038/srep27272 pmid:27255481 pmcid:PMC4891680 fatcat:gfgba3sbrnbvtijyv3g6ojemxq

A Dual Model for Prioritizing Cancer Mutations in the Non-coding Genome Based on Germline and Somatic Events

Jia Li, Marie-Anne Poursat, Damien Drubay, Arnaud Motz, Zohra Saci, Antonin Morillon, Stefan Michiels, Daniel Gautheret, Rachel Karchin
2015 PLoS Computational Biology  
The second (somatic) model estimates tumor mutation density based on whole genome tumor sequencing.  ...  We show that each model reflects a different set of constraints acting either on the normal or tumor genome, and we identify the specific genome features that most contribute to these constraints.  ...  Evolutionary conserved regions, cTFBS and UTRs that were all under strong selective constraints in the germline model present highly variable mutation densities in tumors, with densities ranging from low  ... 
doi:10.1371/journal.pcbi.1004583 pmid:26588488 pmcid:PMC4654583 fatcat:hazojd57erftrcsg2fubyrgcke

Effects of recombination rate and gene density on transposable element distributions in Arabidopsis thaliana

Stephen I Wright, Newton Agrawal, Thomas E Bureau
2003 Genome Research  
In contrast, a consistent negative correlation between gene density and TE abundance, and a strong under-representation of TE insertions in introns suggest that selection against TE disruption of gene  ...  expression is playing a more important role in A. thaliana.  ...  This work was supported by a National Science and Engineering Research Council (NSERC) of Canada operating and Genomics Project grants to T.E.B., and by a Commonwealth fellowship and an NSERC postgraduate  ... 
doi:10.1101/gr.1281503 pmid:12902382 pmcid:PMC403781 fatcat:wfifg2ro2veyhotxpcydxg7ocq

Mobile introns shape the genetic diversity of their host genes [article]

Jelena Repar, Tobias Warnecke
2016 bioRxiv   pre-print
In particular, we show that, in all three species, the density of single nucleotide polymorphisms increases as one approaches a mobile intron.  ...  Instead, our findings implicate intron mobility as a direct driver of host gene diversity.  ...  Acknowledgments We thank John Wolters, Paul Jung, Daniel Jeffares, Jonathan Flowers, Ashley Farlow and Detlef Weigel for sharing sequence data and alignments, and Peter Sarkies and Anita Krisko for comments  ... 
doi:10.1101/092585 fatcat:obywdgbeqjhmzgff75v3ry6n4i

Evolutionary Constraint in Flanking Regions of Avian Genes

Axel Künstner, Benoit Nabholz, Hans Ellegren
2011 Molecular biology and evolution  
Finally, we found that genes evolving under the highest constraint measured by d N /d S also had the highest level of constraint in the 3# flanking region.  ...  Constraint was higher in annotated 3# untranslated regions (UTRs) than in non-UTRs at the same distance from the stop codon and higher in sequences annotated as microRNA (miRNA)-binding sites than in non-miRNA-binding  ...  Acknowledgments Financial support was obtained from the Swedish Research Council, a European Research Council Advanced Investigator Grant, and a Knut and Alice Wallenberg Foundation Wallenberg Scholar  ... 
doi:10.1093/molbev/msr066 pmid:21393603 fatcat:pxktgmtb4nft3a2at7t7bueapi

Human piRNAs Are Under Selection in Africans and Repress Transposable Elements

S. Lukic, K. Chen
2011 Molecular biology and evolution  
We found strong statistical evidence that piRNA sequences are under selective constraint in African populations.  ...  Finally, we observed a significant depletion of piRNA matches in the reverse transcriptase region of the consensus human LINE-1 element but not of the consensus mouse LINE-1 element.  ...  piRNAs Show a Signature of Selective Constraint in African Populations Although piRNAs are not well conserved between species, we reasoned that they might be under detectable selective constraint at a  ... 
doi:10.1093/molbev/msr141 pmid:21613236 pmcid:PMC3199439 fatcat:2vpty44k6jbt3de6d4nozdutiq

Twist-Induced Defects of the P-SSP7 Genome Revealed by Modeling the Cryo-EM Density

Qian Wang, Christopher G. Myers, B. Montgomery Pettitt
2015 Journal of Physical Chemistry B  
Recent cryo-EM experiments find a hole in the density map of P-SSP7 phage, located in the DNA segment filling the portal channel of the phage.  ...  We use experimentally derived structural constraints with coarse-grained simulation techniques to consider contrasting model interpretations of reconstructed density in the portal channel.  ...  Wah Chiu for providing the cryo-EM density map for P-SSP7 phage. The authors also thank Dr. Ouldridge and his colleagues for sharing the orignal code for coarse-grained DNA simulation.  ... 
doi:10.1021/acs.jpcb.5b00865 pmid:25793549 pmcid:PMC4659697 fatcat:ekk4wojp6rgcvbtxewhzj4vm2e

Genomic Diversity and Evolution of Quasispecies in Newcastle Disease Virus Infections

Archana Jadhav, Lele Zhao, Weiwei Liu, Chan Ding, Venugopal Nair, Sebastian E. Ramos-Onsins, Luca Ferretti
2020 Viruses  
Variants in viruses from in vitro samples are mostly localised in non-coding regions and 3′ and 5′ untranslated regions (3′UTRs or 5′UTRs), while in vivo samples contain an order of magnitude more variants  ...  The M sequence is strongly constrained both between and within hosts, fusion protein (F) coding gene is under intra-host positive selection, and NP and HN show contrasting patterns: HN RNA sequence is  ...  The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.  ... 
doi:10.3390/v12111305 pmid:33202558 fatcat:3g3ysx2mazcxlanq65z3us2zsa
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