scholarly journals Fine-Grained Parallel Genomic Sequence Comparison

10.5772/9449 ◽  
2010 ◽  
Author(s):  
Dominique Lavenier
Keyword(s):  
Sequence Comparison ◽  
Genomic Sequence ◽  
Fine Grained

Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori

Nature ◽  
10.1038/16495 ◽  
1999 ◽  
Vol 397 (6715) ◽  
pp. 176-180 ◽  
Author(s):  
Richard A. Alm ◽  
Lo-See L. Ling ◽  
Donald T. Moir ◽  
Benjamin L. King ◽  
Eric D. Brown ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Sequence Comparison ◽  
Genomic Sequence ◽  
Gastric Pathogen

Orion: Scaling Genomic Sequence Matching with Fine-Grained Parallelization

2014 ◽  
Author(s):  
Kanak Mahadik ◽  
Somali Chaterji ◽  
Bowen Zhou ◽  
Milind Kulkarni ◽  
Saurabh Bagchi
Keyword(s):  
Genomic Sequence ◽  
Sequence Matching ◽  
Fine Grained

scholarly journals Adaptive seeds tame genomic sequence comparison

2011 ◽  
Vol 21 (3) ◽  
pp. 487-493 ◽  
Author(s):  
S. M. Kielbasa ◽  
R. Wan ◽  
K. Sato ◽  
P. Horton ◽  
M. C. Frith
Keyword(s):  
Sequence Comparison ◽  
Genomic Sequence

Genomic sequence comparison of the human and mouse adenosine deaminase gene regions

1999 ◽  
Vol 10 (2) ◽  
pp. 95-101 ◽  
Author(s):  
Anthony G. Brickner ◽  
Ben F. Koop ◽  
Bruce J. Aronow ◽  
Dan A. Wiginton
Keyword(s):  
Adenosine Deaminase ◽  
Sequence Comparison ◽  
Genomic Sequence ◽  
Human And Mouse

scholarly journals DQX1, an RNA-dependent ATPase homolog with a novel DEAQ box: expression pattern and genomic sequence comparison of the human and mouse genes

2001 ◽  
Vol 12 (6) ◽  
pp. 456-461 ◽  
Author(s):  
Weizhen Ji ◽  
Feng Chen ◽  
Trang Do ◽  
Anh Do ◽  
Bruce A. Roe ◽  
...  
Keyword(s):  
Expression Pattern ◽  
Sequence Comparison ◽  
Genomic Sequence ◽  
Dependent Atpase ◽  
Human And Mouse

scholarly journals Erratum: Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori

Nature ◽  
10.1038/17837 ◽  
1999 ◽  
Vol 397 (6721) ◽  
pp. 719-719 ◽  
Author(s):  
Richard A. Alm ◽  
Lo-See L. Ling ◽  
Donald T. Moir ◽  
Benjamin L. King ◽  
Eric D. Brown ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Sequence Comparison ◽  
Genomic Sequence ◽  
Gastric Pathogen

scholarly journals Application of Statistical Mirroring in Biological Sequence Analysis

2019 ◽  
Author(s):  
Kabir Bindawa Abdullahi
Keyword(s):  
Sequence Comparison ◽  
Statistical Power ◽  
Genomic Sequence ◽  
Biological Sequence ◽  
Suitable Alternative ◽  
Biological Sequence Analysis ◽  
Free Alternative ◽  
Alignment Free ◽  
Computational Simplicity ◽  
Clustal Omega

Sequence alignment and comparison through pairwise, multiple, global and local techniques are the main principles that underpin comparative genomics. However, most of the algorithms used are alignment-based which imposed some limitations on their use and application. In an attempt to provide an alignment-free alternative approaches, a methodology of comparative optinalysis and statistical mirroring was used and adopted to provide a suitable alternative for multiple genomic sequence comparison. In this article, methods comparison with MUSCLE, MUFFT, Clustal Omega, and T-Coffee was designed to assess the suitability and statistical power of statistical mirroring as an alternative method for multiple genomic sequences comparison using different sets of logically generated biological sequence datasets with different problems and computational complications. The results of the comparisons validate that statistical mirroring is a suitable alignment-free alternative approach for multiple genomic sequence comparison. The applied method (statistical mirroring) distinguishes itself over MUSCLE, MUFFT, Clustal Omega, and T-Coffee in specificity to a position-specific changes, specificity to a base-specific changes, cladogram and phylogenetic linearity, alignment independency, computational simplicity, and limit of input capacity.

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