Whole genome assembly from 454 sequencing output via modified DNA graph concept

Błażewicz, Jacek; Bryja, Marcin; Figlerowicz, Marek; Gawron, Piotr; Kasprzak, Marta; Kirton, Edward; Platt, Darren; Przybytek, Jakub; Świercz, Aleksandra; Szajkowski, Lukasz

doi:10.1016/j.compbiolchem.2009.04.005

Cited by 18 publications

(12 citation statements)

References 22 publications

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“…We have recently invented a new assembly algorithm working very well with the data from 454 sequencer [2], but consuming noticeable amount of time. In this algorithm our ideas from previous approaches to DNA sequencing by hybridization were partially applied [3,6].…”

Section: Algorithmmentioning

confidence: 99%

Dna Sequence Assembly Involving an Acyclic Graph Model

Błażewicz¹,

Frohmberg²,

Gawron³

et al. 2013

Foundations of Computing and Decision Sciences

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The problem of DNA sequence assembly is well known for its high complexity. Experimental errors of different kinds present in data and huge sizes of the problem instances make this problem very hard to solve. In order to deal with such data, advanced efficient heuristics must be constructed. Here, we propose a new approach to the sequence assembly problem, modeled as the problem of searching for paths in an acyclic digraph. Since the graph representing an assembly instance is not acyclic in general, it is heuristically transformed into the acyclic form. This approach reduces the time of computations significantly and allows to maintain high quality of produced solutions.

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Section: Algorithmmentioning

confidence: 99%

Dna Sequence Assembly Involving an Acyclic Graph Model

Błażewicz¹,

Frohmberg²,

Gawron³

et al. 2013

Foundations of Computing and Decision Sciences

Self Cite

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show abstract

“…Jacek Błażewicz directs a large team of researchers, some of whom are affiliated with both institutions. It comprises several groups working on various aspects of computational biology: Marta Kasprzak and Aleksandra Świercz are working on DNA sequencing, assembling and mapping [68] and on microarray data analysis. Piotr Formanowicz conducts research on the application of Petri nets to study metabolic processes [69].…”

Section: Main Bioinformatics Research Centers In Polandmentioning

confidence: 99%

Bioinformatics and Computational Biology in Poland

Bujnicki

Tiuryn

2013

PLoS Comput Biol

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“…While these platforms have enormous breadth in applications, including the newer approaches of ChIP‐seq, transcriptome (Craft et al ., 2010), microRNA discovery (Shi et al ., 2009; Yanmei et al ., 2009) and whole genome resequencing (e.g. Blazewicz et al ., 2009), usability of the outputted reads varies significantly when compared with a Sanger ABI sequencing read length of ∼800 bp and accuracy rate of 99.0% to 99.999% (Table 1). A detailed review is provided by Metzker (2010).…”

Section: Scientific Discoveries Through Technological Advancementmentioning

confidence: 99%

Marine genomics: at the interface of marine microbial ecology and biodiscovery

Heidelberg

Gilbert

Joint

2010

Microbial Biotechnology

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The composition and activities of microbes from diverse habitats have been the focus of intense research during the past decade with this research being spurred on largely by advances in molecular biology and genomic technologies. In recent years environmental microbiology has entered very firmly into the age of the ‘omics’– (meta)genomics, proteomics, metabolomics, transcriptomics – with probably others on the rise. Microbes are essential participants in all biogeochemical processes on our planet, and the practical applications of what we are learning from the use of molecular approaches has altered how we view biological systems. In addition, there is considerable potential to use information about uncultured microbes in biodiscovery research as microbes provide a rich source of discovery for novel genes, enzymes and metabolic pathways. This review explores the brief history of genomic and metagenomic approaches to study environmental microbial assemblages and describes some of the future challenges involved in broadening our approaches – leading to new insights for understanding environmental problems and enabling biodiscovery research.

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Whole genome assembly from 454 sequencing output via modified DNA graph concept

Cited by 18 publications

References 22 publications

Dna Sequence Assembly Involving an Acyclic Graph Model

Dna Sequence Assembly Involving an Acyclic Graph Model

Bioinformatics and Computational Biology in Poland

Marine genomics: at the interface of marine microbial ecology and biodiscovery

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