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Cited By28
Published on Dec 23, 2003in BMC Bioinformatics 2.21
Michael Brudno44
Estimated H-index: 44
(Stanford University),
Michael A. Chapman15
Estimated H-index: 15
(University of Cambridge)
+ 2 AuthorsBurkhard Morgenstern36
Estimated H-index: 36
(Bielefeld University)
Background: Genomic sequence alignment is a powerful method for genome analysis and annotation, as alignments are routinely used to identify functional sites such as genes or regulatory elements. With a growing number of partially or completely sequenced genomes, multiple alignment is playing an increasingly important role in these studies. In recent years, various tools for pair-wise and multiple genomic alignment have been proposed. Some of them are extremely fast, but often efficiency is achi...
153 Citations Source Cite
Published on Dec 4, 2000in Genome Biology 13.21
Jonathan A. Eisen80
Estimated H-index: 80
John F. Heidelberg48
Estimated H-index: 48
+ 1 AuthorsSteven L. Salzberg118
Estimated H-index: 118
Whole-genome comparisons can provide great insight into many aspects of biology. Until recently, however, comparisons were mainly possible only between distantly related species. Complete genome sequences are now becoming available from multiple sets of closely related strains or species. By comparing the recently completed genome sequences of Vibrio cholerae,Streptococcus pneumoniae and Mycobacterium tuberculosis to those of closely related species - Escherichia coli, Streptococcus pyogenes and...
238 Citations Source Cite
Published on Aug 1, 2001in Genome Biology 13.21
Natalia Volfovsky15
Estimated H-index: 15
Brian J. Haas64
Estimated H-index: 64
Steven L. Salzberg118
Estimated H-index: 118
Background A computational system for analysis of the repetitive structure of genomic sequences is described. The method uses suffix trees to organize and search the input sequences; this data structure has been used previously for efficient computation of exact and degenerate repeats.
118 Citations Source Cite
Published on Jan 29, 2004in BMC Bioinformatics 2.21
Estienne C Swart1
Estimated H-index: 1
(South African National Bioinformatics Institute),
Winston Hide47
Estimated H-index: 47
(South African National Bioinformatics Institute),
Cathal Seoighe32
Estimated H-index: 32
(South African National Bioinformatics Institute)
Background Rates of substitution in protein-coding sequences can provide important insights into evolutionary processes that are of biomedical and theoretical interest. Increased availability of coding sequence data has enabled researchers to estimate more accurately the coding sequence divergence of pairs of organisms. However the use of different data sources, alignment protocols and methods to estimate substitution rates leads to widely varying estimates of key parameters that define the codi...
6 Citations Source Cite
Published on Mar 2, 2006in BMC Bioinformatics 2.21
Arthur Chun-Chieh Shih13
Estimated H-index: 13
(Academia Sinica),
D. T. Lee45
Estimated H-index: 45
(Academia Sinica)
+ 7 AuthorsMu Fen Hsieh1
Estimated H-index: 1
(Academia Sinica)
Background Deluged by the rate and complexity of completed genomic sequences, the need to align longer sequences becomes more urgent, and many more tools have thus been developed. In the initial stage of genomic sequence analysis, a biologist is usually faced with the questions of how to choose the best tool to align sequences of interest and how to analyze and visualize the alignment results, and then with the question of whether poorly aligned regions produced by the tool are indeed not homolo...
15 Citations Source Cite
Published on Jul 12, 2005in BMC Bioinformatics 2.21
Hélène Chiapello17
Estimated H-index: 17
I Bourgait1
Estimated H-index: 1
+ 4 AuthorsM El Karoui1
Estimated H-index: 1
Background Public databases now contain multitude of complete bacterial genomes, including several genomes of the same species. The available data offers new opportunities to address questions about bacterial genome evolution, a task that requires reliable fine comparison data of closely related genomes. Recent analyses have shown, using pairwise whole genome alignments, that it is possible to segment bacterial genomes into a common conserved backbone and strain-specific sequences called loops.
41 Citations Source Cite
Published on Dec 1, 2010in BMC Bioinformatics 2.21
Kirill Kryukov5
Estimated H-index: 5
(National Institute of Genetics),
Naruya Saitou43
Estimated H-index: 43
(National Institute of Genetics)
Background Large nucleotide sequence datasets are becoming increasingly common objects of comparison. Complete bacterial genomes are reported almost everyday. This creates challenges for developing new multiple sequence alignment methods. Conventional multiple alignment methods are based on pairwise alignment and/or progressive alignment techniques. These approaches have performance problems when the number of sequences is large and when dealing with genome scale sequences.
12 Citations Source Cite
Published on Jan 1, 2010in BMC Genomics 3.73
Karlene H. Lynch12
Estimated H-index: 12
(University of Alberta),
Paul Stothard33
Estimated H-index: 33
(University of Alberta),
Jonathan J. Dennis25
Estimated H-index: 25
(University of Alberta)
Background The Burkholderia cepacia complex (BCC) is comprised of at least seventeen Gram-negative species that cause infections in cystic fibrosis patients. Because BCC bacteria are broadly antibiotic resistant, phage therapy is currently being investigated as a possible alternative treatment for these infections. The purpose of our study was to sequence and characterize three novel BCC-specific phages: KS5 (vB_BceM-KS5 or vB_BmuZ-ATCC 17616), KS14 (vB_BceM-KS14) and KL3 (vB_BamM-KL3 or vB_BceZ...
35 Citations Source Cite
Published on Jan 1, 2014in BMC Genomics 3.73
Kerry K. Cooper10
Estimated H-index: 10
(United States Department of Agriculture),
Robert E. Mandrell47
Estimated H-index: 47
(United States Department of Agriculture)
+ 7 AuthorsMichelle Qiu Carter11
Estimated H-index: 11
(United States Department of Agriculture)
Background Although serotype O157:H7 is the predominant enterohemorrhagic Escherichia coli (EHEC), outbreaks of non-O157 EHEC that cause severe foodborne illness, including hemolytic uremic syndrome have increased worldwide. In fact, non-O157 serotypes are now estimated to cause over half of all the Shiga toxin-producing Escherichia coli (STEC) cases, and outbreaks of non-O157 EHEC infections are frequently associated with serotypes O26, O45, O103, O111, O121, and O145. Currently, there are no c...
36 Citations Source Cite
Published on Jan 1, 2012in BMC Genomics 3.73
Chi-Ching Lee8
Estimated H-index: 8
(National Tsing Hua University),
Wei-Cheng Lo10
Estimated H-index: 10
(National Chiao Tung University)
+ 3 AuthorsPing-Chiang Lyu35
Estimated H-index: 35
(National Tsing Hua University)
Background Microorganisms able to grow under artificial culture conditions comprise only a small proportion of the biosphere's total microbial community. Until recently, scientists have been unable to perform thorough analyses of difficult-to-culture microorganisms due to limitations in sequencing technology. As modern techniques have dramatically increased sequencing rates and rapidly expanded the number of sequenced genomes, in addition to traditional taxonomic classifications which focus on t...
4 Citations Source Cite
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