16 papers · ranked by Valyu relevance
Xiao-Long Wu, Yun Heo, Izzat El Hajj, Wen-Mei Hwu + 2 more
'Jian Ma'] Background With the cost reduction of the next-generation sequencing (NGS) technologies, genomics has provided us with an unprecedented opportunity to understand fundamental questions in biology and elucidate human diseases. De novo genome assembly is one of the most important steps to reconstruct the…
Mohammed Sahli, Tetsuo Shibuya
Background Genome assembly is considered to be a challenging problem in computational biology, and has been studied extensively by many researchers. It is extremely difficult to build a general assembler that is able to reconstruct the original sequence instead of many contigs. However, we believe that creating…
Chengxi Ye, Zhanshan Sam Ma, Charles H Cannon, Mihai Pop + 1 more
'Douglas W Yu'] Background The very large memory requirements for the construction of assembly graphs for de novo genome assembly limit current algorithms to super-computing environments. Methods In this paper, we demonstrate that constructing a sparse assembly graph which stores only a small fraction of the observed…
Chunyu Wang, Maozu Guo, Xiaoyan Liu, Yang Liu + 1 more
DNA sequencing technology has been rapidly evolving, and produces a large number of short reads with a fast rising tendency. This has led to a resurgence of research in whole genome shotgun assembly algorithms. We start the assembly algorithm by clustering the short reads in a cloud computing framework, and the…
Katarzyna Nałęcz-Charkiewicz, Robert M. Nowak
Background The assembly task is an indispensable step in sequencing genomes of new organisms and studying structural genomic changes. In recent years, the dynamic development of next-generation sequencing (NGS) methods raises hopes for making whole-genome sequencing a fast and reliable tool used, for example, in…
Ian Seet, Keith Y. Patarroyo, Gage Siebert, Sara I. Walker + 1 more
of the Assembly Chemical Space of Molecular Graphs Authors: Ian Seet, Keith Y. Patarroyo, Gage Siebert, Sara I. Walker, Leroy Cronin Quantifying how hard it is to build a molecular graph matters for biosignature detection, chemical complexity, and cheminformatics. We present an exact, scalable algorithm to compute the…
Zeinab Taghavi
Background Acquiring genomes at single-cell resolution has many applications such as in the study of microbiota. However, deep sequencing and assembly of all of millions of cells in a sample is prohibitively costly. A property that can come to rescue is that deep sequencing of every cell should not be necessary to…
Abhishek Sharma, Dániel Czégel, Michael Lachmann, Christopher P. Kempes + 2 more
'Christopher P. Kempes' 'Sara I. Walker' 'Leroy Cronin'] Scientists have grappled with reconciling biological evolution1,2 with the immutable laws of the Universe defined by physics. These laws underpin life’s origin, evolution and the development of human culture and technology, yet they do not predict the emergence…
Vamsi K Kundeti, Sanguthevar Rajasekaran, Hieu Dinh, Matthew Vaughn + 1 more
'Vishal Thapar'] Background Assembling genomic sequences from a set of overlapping reads is one of the most fundamental problems in computational biology. Algorithms addressing the assembly problem fall into two broad categories - based on the data structures which they employ. The first class uses an overlap/string…
Tyler G. Moore, Max H. Garzon, Russell J. Deaton, Ming Dao
Inspired by biological systems, self-assembly aims to construct complex structures. It functions through piece-wise, local interactions among component parts and has the potential to produce novel materials and devices at the nanoscale. Algorithmic self-assembly models the product of self-assembly as the output of some…
Haihe Shi, Xuchu Zhang
In recent years, there has been an explosive increase in the amount of bioinformatics data produced, but data are not information. The purpose of bioinformatics research is to obtain information with biological significance from large amounts of data. Multiple sequence alignment is widely used in sequence homology…
Felipe A. Louza, Guilherme P. Telles, Steve Hoffmann, Cristina D. A. Ciferri
'Cristina D. A. Ciferri'] Background Suffix arrays, augmented by additional data structures, allow solving efficiently many string processing problems. The external memory construction of the generalized suffix array for a string collection is a fundamental task when the size of the input collection or the data…
Joël Lindegger, Damla Senol Cali, Mohammed Alser, Juan Gómez-Luna + 3 more
Pairwise sequence alignment is a computational step commonly required in bioinformatics pipelines (), such as in read mapping () and de novo assembly (). We formulate the problem as: (i) finding the edit distance between two sequences () and (ii) determining the sequence of corresponding edits. Efficient algorithms for…
Christopher P. Kempes, Michael Lachmann, Andrew Iannaccone, G. Matthew Fricke + 3 more
'G. Matthew Fricke' 'M. Redwan Chowdhury' 'Sara I. Walker' 'Leroy Cronin'] Assembly theory (AT) quantifies selection using the assembly equation, identifying complex objects through the assembly index, the minimal steps required to build an object from basic parts, and copy number, the observed instances of the object.…
Arash Bayat, Bruno Gaëta, Aleksandar Ignjatovic, Sri Parameswaran
Background Pairwise alignment of short DNA sequences with affine-gap scoring is a common processing step performed in a range of bioinformatics analyses. Dynamic programming (i.e. Smith-Waterman algorithm) is widely used for this purpose. Despite using data level parallelisation, pairwise alignment consumes much time.…
Fabio F. de Oliveira, Leonardo A. Dias, Marcelo A. C. Fernandes, Slavisa Jovanovic
'Slavisa Jovanovic'] In bioinformatics, alignment is an essential technique for finding similarities between biological sequences. Usually, the alignment is performed with the Smith-Waterman (SW) algorithm, a well-known sequence alignment technique of high-level precision based on dynamic programming. However, given…