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Beyond Adjacency Maximization: Scaffold Filling for New String Distances

Laurent Bulteau, Guillaume Fertin, Christian Komusiewicz, Marc Herbstritt
2017 Annual Symposium on Combinatorial Pattern Matching  
: the first generalizes the notion of common adjacencies by maximizing the number of common k-mers between S * and G (k-Mer Scaffold Filling), the second aims at minimizing the number of breakpoints between  ...  We also show that Min-Breakpoint Scaffold Filling is FPT wrt. a parameter combining the number of missing genes, the number of gene repetitions and the target distance.  ...  Since there is no breakpoint before u, f j C P M 2 0 1 7 27:12 Beyond Adjacency Maximization: Scaffold Filling for New String Distances must be inserted after a contig ending with u .  ... 
doi:10.4230/lipics.cpm.2017.27 dblp:conf/cpm/BulteauFK17 fatcat:huixer4v45dstdincbngdrlqsu

Networks beyond pairwise interactions: structure and dynamics [article]

Federico Battiston, Giulia Cencetti, Iacopo Iacopini, Vito Latora, Maxime Lucas, Alice Patania, Jean-Gabriel Young, Giovanni Petri
2020 arXiv   pre-print
Here, we present a complete overview of the emerging field of networks beyond pairwise interactions.  ...  We focus on novel emergent phenomena characterizing landmark dynamical processes, such as diffusion, spreading, synchronization and games, when extended beyond pairwise interactions.  ...  filled in.  ... 
arXiv:2006.01764v1 fatcat:h4ezvequxrbyrozpjbb6lbqhj4

Cerulean: A hybrid assembly using high throughput short and long reads [article]

Viraj Deshpande, Eric DK Fung, Son Pham, Vineet Bafna
2013 arXiv   pre-print
In contrast to the state-of-the-art long reads error correction technique, which requires high computational resources and long running time on a supercomputer even for bacterial genome datasets, our software  ...  Acknowledgments The authors will like to sincerely thank Pavel Pevzner and Glenn Tesler for their insightful comments.  ...  Thus, the final scaffolds can be inferred from these annotated paths on the corresponding sequence of reads that are used for gap filling.  ... 
arXiv:1307.7933v1 fatcat:vcxid2rr7vgjzgw5omkxv2urou

Networks beyond pairwise interactions: Structure and dynamics

Federico Battiston, Giulia Cencetti, Iacopo Iacopini, Vito Latora, Maxime Lucas, Alice Patania, Jean-Gabriel Young, Giovanni Petri
2020 Physics reports  
We focus in particular on new emergent phenomena characterizing dynamical processes, such as diffusion, synchronization, spreading, social dynamics and games, when extended beyond pairwise interactions  ...  Here we present a complete overview of the emerging field of networks beyond pairwise interactions.  ...  filled in.  ... 
doi:10.1016/j.physrep.2020.05.004 fatcat:pkugz4i5obainmcrwod6i4od7q

The MaSuRCA genome assembler

Aleksey V. Zimin, Guillaume Marçais, Daniela Puiu, Michael Roberts, Steven L. Salzberg, James A. Yorke
2013 Bioinformatics  
Results: We evaluate the performance of MaSuRCA against two of the most widely used assemblers for Illumina data, Allpaths-LG and SOAPdenovo2, on two datasets from organisms for which high-quality assemblies  ...  In particular, multiple algorithms based on de Bruijn graphs have been shown to be effective for the assembly problem.  ...  ACKNOWLEDGEMENTS We thank Kristian Stevens (University of California-Davis) for his helpful comments.  ... 
doi:10.1093/bioinformatics/btt476 pmid:23990416 pmcid:PMC3799473 fatcat:27yj6p6osng6be2tbi2lwikkha

GAML: genome assembly by maximum likelihood

Vladimír Boža, Broňa Brejová, Tomáš Vinař
2015 Algorithms for Molecular Biology  
Resolution of repeats and scaffolding of shorter contigs are critical parts of genome assembly.  ...  Results: We propose a new framework that allows systematic combination of diverse sequencing datasets into a single assembly.  ...  The authors would like to thank Viraj Deshpande for sharing his research data. An early version of this paper was published in WABI 2014 conference proceedings.  ... 
doi:10.1186/s13015-015-0052-6 pmid:26042154 pmcid:PMC4454275 fatcat:nvgmikbkjveb3ir5hmzjwyddfa

GAML: Genome Assembly by Maximum Likelihood [chapter]

Vladimír Boža, Broňa Brejová, Tomáš Vinař
2014 Lecture Notes in Computer Science  
Resolution of repeats and scaffolding of shorter contigs are critical parts of genome assembly.  ...  Results: We propose a new framework that allows systematic combination of diverse sequencing datasets into a single assembly.  ...  The authors would like to thank Viraj Deshpande for sharing his research data. An early version of this paper was published in WABI 2014 conference proceedings.  ... 
doi:10.1007/978-3-662-44753-6_10 fatcat:wntsodclnvc2zpskc3o5mnwa64

A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds

Andreas Wallberg, Ignas Bunikis, Olga Vinnere Pettersson, Mai-Britt Mosbech, Anna K. Childers, Jay D. Evans, Alexander S. Mikheyev, Hugh M. Robertson, Gene E. Robinson, Matthew T. Webster
2019 BMC Genomics  
The new assembly (Amel_HAv3) is significantly more contiguous and complete than the previous one (Amel_4.5), based mainly on Sanger sequencing reads.  ...  Conclusions: The improved assembly will be of utility for refining gene models, studying genome function, mapping functional genetic variation, identification of structural variants, and comparative genomics  ...  Sullivan (Phase Genomics) for assistance with the Hi-C data.  ... 
doi:10.1186/s12864-019-5642-0 fatcat:kcciknssg5hnnjynukdszrzi7i

Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence

Susan E Celniker, David A Wheeler, Brent Kronmiller, Joseph W Carlson, Aaron Halpern, Sandeep Patel, Mark Adams, Mark Champe, Shannon P Dugan, Erwin Frise, Ann Hodgson, Reed A George (+20 others)
2002 Genome Biology  
In the current version of the 116.9 Mb euchromatic genome, called Release 3, the six euchromatic chromosome arms are represented by 13 scaffolds with a total of 37 sequence gaps.  ...  The sequence we report here, Release 3, is a reliable resource for molecular genetic experimentation and computational analysis.  ...  We are indebted to David Gordon for his continual modifications to Consed. We thank Harald Biessmann for helpful discussions concerning telomeres.  ... 
pmid:12537568 pmcid:PMC151181 fatcat:m6myjq5q25fupckcnzz56bvcny

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Susan E Celniker, David A Wheeler, Brent Kronmiller, Joseph W Carlson, Aaron Halpern, Sandeep Patel, Mark Adams, Mark Champe, Shannon P Dugan, Erwin Frise, Ann Hodgson, Reed A George (+20 others)
2016 Genome Biology  
In the current version of the 116.9 Mb euchromatic genome, called Release 3, the six euchromatic chromosome arms are represented by 13 scaffolds with a total of 37 sequence gaps.  ...  And, how difficult is it to bring a WGS sequence to the accepted standard for finished sequence? We are now in a position to answer these questions.  ...  We are indebted to David Gordon for his continual modifications to Consed. We thank Harald Biessmann for helpful discussions concerning telomeres.  ... 
doi:10.1186/gb-2002-3-12-research0079 fatcat:fddqtb6gubcrtnfpz2dxdlbjee

A hybrid de novo genome assembly of the honeybee, Apis mellifera , with chromosome-length scaffolds [article]

Andreas Wallberg, Ignas Bunikis, Olga Vinnere Pettersson, Mai-Britt Mosbech, Anna K Childers, Jay D Evans, Alexander S Mikheyev, Hugh M Robertson, Gene E Robinson, Matthew T Webster
2018 bioRxiv   pre-print
The new assembly (Amel_HAv3) is significantly more contiguous and complete than the previous one (Amel_4.5), based mainly on Sanger sequencing reads.  ...  Conclusions: The improved assembly will be of utility for refining gene models, studying genome function, mapping functional genetic variation, identification of structural variants, and comparative genomics  ...  Sullivan (Phase Genomics) for assistance with the Hi-C data.  ... 
doi:10.1101/361469 fatcat:6mh6wfxnl5av7crc5wzuxrenfu

Shotgun Sequence Assembly [chapter]

Mihai Pop
2004 Advances in Computers  
Shotgun sequencing is the most widely used technique for determining the DNA sequence of organisms.  ...  In the case of an assembly with N 2 scaffolds we need to determine the adjacency information for N different scaffold ends.  ...  In order to reduce the effect of errors scaffolders require at least two links between adjacent contigs.  ... 
doi:10.1016/s0065-2458(03)60006-9 fatcat:6urpjmehrfdnbp4c6ij5vmcpge

Differentiable Scaffolding Tree for Molecular Optimization [article]

Tianfan Fu, Wenhao Gao, Cao Xiao, Jacob Yasonik, Connor W. Coley, Jimeng Sun
2022 arXiv   pre-print
To address this, we propose differentiable scaffolding tree (DST) that utilizes a learned knowledge network to convert discrete chemical structures to locally differentiable ones.  ...  Sampling from DST Then we sample the new scaffolding tree from the optimized DST.  ...  Both topology and substructure to fill are sampled from the optimized differentiable scaffolding tree, as shown in Equation (11) . This is what we use in this paper. • "random + DPP".  ... 
arXiv:2109.10469v2 fatcat:yo3r5k5rzfhdzdr2bcw3mfhimi

The Atlas Genome Assembly System

P. Havlak
2004 Genome Research  
Atlas was used to assemble a draft DNA sequence of the rat genome; its major components including overlapper and split-scaffold are also being used in pure WGS projects.  ...  The BAC clones afford advantages of localized assembly with reduced computational load, and provide a robust method for dealing with repeated sequences.  ...  College of Wisconsin) for assistance with the rat radiation hybrid map.  ... 
doi:10.1101/gr.2264004 pmid:15060016 pmcid:PMC383319 fatcat:jbusuopcffe2dcscfj5strn3km

Zipper assembly of SHJ photosystems: focus on red naphthalenediimides, optoelectronic finetuning and topological matching

Rajesh Bhosale, Ravuri S. K. Kishore, Velayutham Ravikumar, Oksana Kel, Eric Vauthey, Naomi Sakai, Stefan Matile
2010 Chemical Science  
, and to evaluate their usefulness for zipper assembly of artificial photosystems.  ...  objective of this study was to synthesize multichromophoric donor-acceptor systems with non-halogenated red (R O ) naphthalenediimides (NDIs) attached along p-oligophenyl (POP) and oligophenylethynyl (OPE) scaffolds  ...  Hopfgartner for MS measurements, and the University of Geneva and the Swiss NSF for financial support.  ... 
doi:10.1039/c0sc00177e fatcat:czzfwi2zozdkjmfgpkfm76lc2u
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