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Efficient algorithms for analyzing segmental duplications with deletions and inversions in genomes

Crystal L Kahn, Shay Mozes, Benjamin J Raphael
2010 Algorithms for Molecular Biology  
Segmental duplications, or low-copy repeats, are common in mammalian genomes. In the human genome, most segmental duplications are mosaics comprised of multiple duplicated fragments.  ...  This distance models the process of repeated aggregation and duplication. We also describe extensions of this distance to include certain types of substring deletions and inversions.  ...  BJR is supported by a Career Award at the Scientific Interface from the Burroughs Wellcome Fund and by funding from the ADVANCE Program at Brown University, under NSF Grant No. 0548311.  ... 
doi:10.1186/1748-7188-5-11 pmid:20047668 pmcid:PMC2820476 fatcat:qlhu5xzc5jhsze4gisrqz2phcy

Resolving complex structural genomic rearrangements using a randomized approach

Xuefang Zhao, Sarah B. Emery, Bridget Myers, Jeffrey M. Kidd, Ryan E. Mills
2016 Genome Biology  
Complex chromosomal rearrangements are structural genomic alterations involving multiple instances of deletions, duplications, inversions, or translocations that co-occur either on the same chromosome  ...  We present SVelter, an algorithm that identifies regions of the genome suspected to harbor a complex event and then resolves the structure by iteratively rearranging the local genome structure, in a randomized  ...  Authors' contributions XZ developed and implemented the algorithms and wrote the source code. REM conceived the analytical framework, devised the experiments and supervised the project.  ... 
doi:10.1186/s13059-016-0993-1 pmid:27287201 pmcid:PMC4901421 fatcat:dgj4a6sqxrhctogtyah72wczhq

Resolving Complex Structural Genomic Rearrangements using a Randomized Approach [article]

Xuefang Zhao, Sarah B. Emery, Bridget Myers, Jeffrey M. Kidd, Ryan E. Mills
2015 bioRxiv   pre-print
We present SVelter, an algorithm that first identifies regions of the genome suspected to harbor a complex event and then iteratively rearranges the local genome structure, in a randomized fashion, with  ...  Complex chromosomal rearrangements consist of structural genomic alterations involving multiple instances of deletions, duplications, inversions, or translocations that co-occur either on the same chromosome  ...  duplications, deletions, and inversions ( Figure 4E ).  ... 
doi:10.1101/028217 fatcat:keg6qwervzc6vauejrth6zmeiu

Discovery of tandem and interspersed segmental duplications using high throughput sequencing

Arda Soylev, Thong Le, Hajar Amini, Can Alkan, Fereydoun Hormozdiari, Bonnie Berger
2019 Bioinformatics  
In fact, complex SVs are of crucial importance and several have been associated with genomic disorders.  ...  duplications and gene conversions in direct orientation may be called as simple deletions.  ...  Chaisson for providing PacBio call sets for CHM1 and CHM13, and also the local assembly of these genomes.  ... 
doi:10.1093/bioinformatics/btz237 pmid:30937433 pmcid:PMC6792081 fatcat:f3du5pe4yfdhpd2nldqzdlqj7u

Discovery of tandem and interspersed segmental duplications using high throughput sequencing [article]

Arda Soylev, Thong Le, Hajar Amini, Can Alkan, Fereydoun Hormozdiari
2018 bioRxiv   pre-print
In fact, complex SVs are of crucial importance and several have been associated with genomic disorders.  ...  and gene conversions in direct orientation may be called as simple deletions.  ...  We would also like to Mark Chaisson for providing PacBio call sets for CHM1 and CHM13, and the local assembly of these genomes.  ... 
doi:10.1101/393694 fatcat:4glkzcs3nrf7llntjeoozsjxma

Current analysis platforms and methods for detecting copy number variation

Wenli Li, Michael Olivier
2013 Physiological Genomics  
Current analysis platforms and methods for detecting copy number variation.  ...  of CNVs (e.g., insertions, deletions, duplications, and inversions), and the various mechanisms that create CNVs.  ...  a breakpoint and genotype of an insertion is limited by the read length 23, 45, 61 Read-depth Deletions and duplications Detects very large deletions and duplications Cannot detect inversions  ... 
doi:10.1152/physiolgenomics.00082.2012 pmid:23132758 pmcid:PMC3544484 fatcat:l5lj7p2djndh3oaokc2zafhcae

SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes

Yue Shen, Giovanni Stracquadanio, Yun Wang, Kun Yang, Leslie A. Mitchell, Yaxin Xue, Yizhi Cai, Tai Chen, Jessica S. Dymond, Kang Kang, Jianhui Gong, Xiaofan Zeng (+9 others)
2015 Genome Research  
After proceeding with the copy number estimation algorithm below, the average read depth for deleted segments was 0.27 and the maximum was 4.98.  ...  Algorithms based on Eulerian cycles have become standard in DNA sequence assembly, with many efficient methods (Schatz et al. 2010) .  ... 
doi:10.1101/gr.193433.115 pmid:26566658 pmcid:PMC4691749 fatcat:lrbt62kitrcvrgg7edmpx7rqxu

Decoding the Genomic Architecture of Mammalian and Plant Genomes: Synteny Blocks and Large-scale Duplications

Max A. Alekseyev, Qian Peng, Pavel A. Pevzner, Glenn Tesler
2010 Communications in Information and Systems  
The existing synteny block generation algorithms in plants do not address the issue of generating non-overlapping synteny blocks suitable for analyzing rearrangements and evolution history of duplications  ...  blocks in plant genomes as compared to vertebrate genomes (and especially to mammalian genomes) where segmental duplications are less prevalent and can therefore be largely ignored while constructing  ...  We thank Haixu Tang for providing the RepeatGluer code for A-Bruijn graph construction. We thank Joseph R. Ecker for insightful comments.  ... 
doi:10.4310/cis.2010.v10.n1.a1 fatcat:6pebbrgi3rfavbjgmjy2li4arq

Operon-based approach for the inference of rRNA and tRNA evolutionary histories in bacteria

Tomasz Pawliszak, Meghan Chua, Carson K. Leung, Olivier Tremblay-Savard
2020 BMC Genomics  
In bacterial genomes, rRNA and tRNA genes are often organized into operons, i.e. segments of closely located genes that share a single promoter and are transcribed as a single unit.  ...  Since operons can move around in the genome but are rarely transformed (e.g. rarely broken into different parts), this approach allows for a better inference of orthologous genes in genomes that have been  ...  Acknowledgements The authors wish to thank Adam Grabowiecki, Chamath Welihinda and Michelle Wiebe for their help with the tools developed for data collection and preliminary analyses.  ... 
doi:10.1186/s12864-020-6612-2 pmid:32299351 fatcat:uid72iw7ebda7plgu2cvsxztn4

A geometric approach for classification and comparison of structural variants

S. Sindi, E. Helman, A. Bashir, B. J. Raphael
2009 Bioinformatics  
Motivation: Structural variants, including duplications, insertions, deletions and inversions of large blocks of DNA sequence, are an important contributor to human genome variation.  ...  We derive a computational geometry algorithm to efficiently identify all such intersections. We apply GASV to sequencing data from nine individual human genomes and several cancer genomes.  ...  ACKNOWLEDGEMENTS We thank Franco Preparata and Crystal Kahn for helpful technical discussions, and Anna Ritz for assistance in preparing the manuscript. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btp208 pmid:19477992 pmcid:PMC2687962 fatcat:xqi2kgsa6fftzftj4duql45zbe

Rearrangements and chromosomal evolution

David Sankoff
2003 Current Opinion in Genetics and Development  
These developments provide challenges to computational biologists to refine, revise and scale up mathematical models and algorithms for analyzing genome rearrangements. Addresses  ...  breakpoints in chromosomal regions, the relative importance of genome doubling in the history of multicellular eukaryotes, and of lateral transfer versus gene gain and loss in prokaryotes.  ...  The author is a Fellow of the Program in Evolutionary Biology of the Canadian Institute for Advanced Research and holds the Canada Research Chair in Mathematical Genomics.  ... 
doi:10.1016/j.gde.2003.10.006 pmid:14638318 fatcat:yl3ptudl4jdcjcj5fgh2tw2f3y

SIMULTANEOUS HISTORY RECONSTRUCTION FOR COMPLEX GENE CLUSTERS IN MULTIPLE SPECIES

YU ZHANG, GILTAE SONG, CHIH-HAO HSU, WEBB MILLER
2008 Biocomputing 2009  
Genomic intervals that contain a cluster of similar genes are of extreme biological interest, but difficult to sequence and analyze.  ...  An implementation of the method is evaluated using (1) artificial datasets generated by simulating the operations of duplication, deletion, and speciation starting with featureless "ancestral" sequences  ...  We consider tandem and non-tandem duplications, duplications with inversions, deletions, and speciation events.  ... 
doi:10.1142/9789812836939_0016 fatcat:6inqbwzu2ndnnkhtshq7szkc4i

Simultaneous history reconstruction for complex gene clusters in multiple species

Yu Zhang, Giltae Song, Chih-Hao Hsu, Webb Miller
2009 Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  
Genomic intervals that contain a cluster of similar genes are of extreme biological interest, but difficult to sequence and analyze.  ...  An implementation of the method is evaluated using (1) artificial datasets generated by simulating the operations of duplication, deletion, and speciation starting with featureless "ancestral" sequences  ...  We consider tandem and non-tandem duplications, duplications with inversions, deletions, and speciation events.  ... 
pmid:19209701 pmcid:PMC2758231 fatcat:yzbp2j2y7vgttdqm5zupbkytpi

Detecting structural variations in the human genome using next generation sequencing

R. Xi, T.-M. Kim, P. J. Park
2010 Briefings in Functional Genomics  
In this review, we will describe some of the sequencing-based algorithms for detection of structural variations and discuss the key issues in future development.  ...  Structural variations are widespread in the human genome and can serve as genetic markers in clinical and evolutionary studies.  ...  This work was supported by the US National Institutes of Health (grants RC1 HG005482 and R01 GM082798 to P.J.P.).  ... 
doi:10.1093/bfgp/elq025 pmid:21216738 pmcid:PMC3080742 fatcat:l4cfk3wj4bcqpd6geqwgl2vkdu

Sorting cancer karyotypes using double-cut-and-joins, duplications and deletions

Ron Zeira, Ron Shamir, Oliver Stegle
2018 Bioinformatics  
Results: Here we present a model for the evolution of genomes with multiple gene copies using the operation types double-cut-and-joins, duplications and deletions.  ...  In contrast, tumor genomes also undergo numerical changes such as deletions and duplications, and thus the number of copies of genes varies.  ...  Funding Study supported in part by the Bella Walter Memorial Fund of the Israel Cancer Association and by Len Blavatnik and the Blavatnik Family foundation.  ... 
doi:10.1093/bioinformatics/bty381 pmid:29726899 fatcat:6m6bmifjpvcqpns7gedilpbteu
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