An Approach to Parallel Algorithms for Long DNA Sequences Alignment on Manycore Architecture

2020 ◽  
Vol 27 (8) ◽  
pp. 1248-1252
Author(s):  
Evaldo Bezerra Costa ◽  
Gabriel Pereira Silva ◽  
Marcello Goulart Teixeira
Keyword(s):  
Parallel Algorithms ◽  
Dna Sequences ◽  
Sequences Alignment

scholarly journals PARODS—a study of parallel algorithms for ordering DNA sequences

1996 ◽  
Vol 12 (4) ◽  
pp. 269-280
Author(s):  
Suchendra M. Bhandarkar ◽  
Sridhar Chirravuri ◽  
Jonathan Arnold
Keyword(s):  
Parallel Algorithms ◽  
Dna Sequences

scholarly journals DNA sequences alignment in multi-GPUs: acceleration and energy payoff

2018 ◽  
Vol 19 (S14) ◽  
Author(s):  
Jesús Pérez-Serrano ◽  
Edans Sandes ◽  
Alba Cristina Magalhaes Alves de Melo ◽  
Manuel Ujaldón
Keyword(s):  
Dna Sequences ◽  
Sequences Alignment

PARALLEL ALGORITHMS FOR MAPPING SHORT DEGENERATE AND WEIGHTED DNA SEQUENCES TO A REFERENCE GENOME

2012 ◽  
Vol 23 (02) ◽  
pp. 249-259
Author(s):  
COSTAS S. ILIOPOULOS ◽  
MIRKA MILLER ◽  
SOLON P. PISSIS
Keyword(s):  
Parallel Algorithms ◽  
Dna Sequences ◽  
Message Passing ◽  
Large Scale ◽  
Reference Genome ◽  
Single Experiment ◽  
Sequencing Technologies ◽  
Mapping Process ◽  
Specific Position ◽  
Parallelism Model

One of the most ambitious trends in current biomedical research is the large-scale genomic sequencing of patients. Novel high-throughput (or next-generation) sequencing technologies have redefined the way genome sequencing is performed. They are able to produce millions of short sequences (reads) in a single experiment, and with a much lower cost than previously possible. Due to this massive amount of data, efficient algorithms for mapping these sequences to a reference genome are in great demand, and recently, there has been ample work for publishing such algorithms. One important feature of these algorithms is the support of multithreaded parallel computing in order to speedup the mapping process. In this paper, we design parallel algorithms, which make use of the message-passing parallelism model, to address this problem efficiently. The proposed algorithms also take into consideration the probability scores assigned to each base for occurring in a specific position of a sequence. In particular, we present parallel algorithms for mapping short degenerate and weighted DNA sequences to a reference genome.

Trace Back Optimization For DNA Sequences Alignment Using Viterbi Algorithm

2013 ◽  
Author(s):  
Nur Farah Ain Saliman ◽  
Nur Dalilah Ahmad Sabri ◽  
Syed Abdul Mutalib Al Junid ◽  
Abdul Karimi Halim ◽  
Zulkifli Abd. Majid ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Viterbi Algorithm ◽  
Trace Back ◽  
Sequences Alignment

Transcription factor/DNA interactions visualized by electron spectroscopic imaging

1992 ◽  
Vol 50 (1) ◽  
pp. 450-451
Author(s):  
David P. Bazett-Jones ◽  
Mark L. Brown
Keyword(s):  
Transcription Factor ◽  
Dna Sequences ◽  
Transcription Initiation ◽  
Molecular Mechanisms ◽  
Phosphorus Content ◽  
Spectroscopic Imaging ◽  
Electron Spectroscopic Imaging ◽  
Dna Backbone ◽  
Two Parameters ◽  
High Level

A multisubunit RNA polymerase enzyme is ultimately responsible for transcription initiation and elongation of RNA, but recognition of the proper start site by the enzyme is regulated by general, temporal and gene-specific trans-factors interacting at promoter and enhancer DNA sequences. To understand the molecular mechanisms which precisely regulate the transcription initiation event, it is crucial to elucidate the structure of the transcription factor/DNA complexes involved. Electron spectroscopic imaging (ESI) provides the opportunity to visualize individual DNA molecules. Enhancement of DNA contrast with ESI is accomplished by imaging with electrons that have interacted with inner shell electrons of phosphorus in the DNA backbone. Phosphorus detection at this intermediately high level of resolution (≈lnm) permits selective imaging of the DNA, to determine whether the protein factors compact, bend or wrap the DNA. Simultaneously, mass analysis and phosphorus content can be measured quantitatively, using adjacent DNA or tobacco mosaic virus (TMV) as mass and phosphorus standards. These two parameters provide stoichiometric information relating the ratios of protein:DNA content.

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