ClustalW-MPI: ClustalW analysis using distributed and parallel computing

Li, Kuo Bin

doi:10.1093/bioinformatics/btg192

Cited by 409 publications

(282 citation statements)

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“…Sequences were compared with those in the databases using BLAST (NBCI, URL http://www.ncbi.nlm.nih.gov/BLAST/). The amino-acid sequences were aligned using ClustalW (Li, 2003) and inspected manually with the Genedoc program v. 2.6 (Nicholas et al, 1997). The phylogenetic tree was constructed with the Treecon program package (Van de Peer and De Wachter, 1994) using evolutionary distances (Tajima and Nei, 1984) and the neighbour-joining method (Saitou and Nei, 1987).…”

Section: Resultsmentioning

confidence: 99%

High aromatic ring-cleavage diversity in birch rhizosphere: PAH treatment-specific changes of I.E.3 group extradiol dioxygenases and 16S rRNA bacterial communities in soil

Sipilä

Keskinen²,

Akerman³

et al. 2008

The ISME Journal

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Genes encoding key enzymes of catabolic pathways can be targeted by DNA fingerprinting to explore genetic degradation potential in pristine and polluted soils. We performed a greenhouse microcosm experiment to elucidate structural and functional bacterial diversity in polyaromatic hydrocarbon (PAH)-polluted soil and to test the suitability of birch (Betula pendula) for remediation. Degradation of PAHs was analysed by high-performance liquid chromatography, DNA isolated from soil amplified and fingerprinted by restriction fragment length polymorphism (RFLP) and terminal restriction fragment length polymorphism (T-RFLP). Bacterial 16S rRNA T-RFLP fingerprinting revealed a high structural bacterial diversity in soil where PAH amendment altered the general community structure as well as the rhizosphere community. Birch augmented extradiol dioxygenase diversity in rhizosphere showing a rhizosphere effect, and further pyrene was more efficiently degraded in planted pots. Degraders of aromatic compounds upon PAH amendment were shown by the changed extradiol ring-cleavage community structure in soil. The RFLP analysis grouped extradiol dioxygenase marker genes into 17 distinct operational taxonomic units displaying novel phylogenetic clusters of ring-cleavage dioxygenases representing putative catabolic pathways, and the peptide sequences contained conserved amino-acid signatures of extradiol dioxygenases. A branch of major environmental TS cluster was identified as being related to Parvibaculum lavantivorans ring-cleavage dioxygenase. The described structural and functional diversity demonstrated a complex interplay of bacteria in PAH pollution. The findings improve our understanding of rhizoremediation and unveil the extent of uncharacterized enzymes and may benefit bioremediation research by facilitating the development of molecular tools to detect and monitor populations involved in degradative processes.

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Section: Resultsmentioning

confidence: 99%

High aromatic ring-cleavage diversity in birch rhizosphere: PAH treatment-specific changes of I.E.3 group extradiol dioxygenases and 16S rRNA bacterial communities in soil

Sipilä

Keskinen²,

Akerman³

et al. 2008

The ISME Journal

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“…Codon alignments were derived from protein alignments using customized PERL scripts based on BioPerl (Stajich et al 2002). Whole-plasmid sequence alignments were obtained by using ClustalW-MPI (Li 2003).…”

Section: Methodsmentioning

confidence: 99%

Pervasive Recombination and Sympatric Genome Diversification Driven by Frequency-Dependent Selection in Borrelia burgdorferi, the Lyme Disease Bacterium

Vargas²,

et al. 2011

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How genomic diversity within bacterial populations originates and is maintained in the presence of frequent recombination is a central problem in understanding bacterial evolution. Natural populations of Borrelia burgdorferi, the bacterial agent of Lyme disease, consist of diverse genomic groups co-infecting single individual vertebrate hosts and tick vectors. To understand mechanisms of sympatric genome differentiation in B. burgdorferi, we sequenced and compared 23 genomes representing major genomic groups in North America and Europe. Linkage analysis of .13,500 single-nucleotide polymorphisms revealed pervasive horizontal DNA exchanges. Although three times more frequent than point mutation, recombination is localized and weakly affects genome-wide linkage disequilibrium. We show by computer simulations that, while enhancing population fitness, recombination constrains neutral and adaptive divergence among sympatric genomes through periodic selective sweeps. In contrast, simulations of frequency-dependent selection with recombination produced the observed pattern of a large number of sympatric genomic groups associated with major sequence variations at the selected locus. We conclude that negative frequency-dependent selection targeting a small number of surface-antigen loci (ospC in particular) sufficiently explains the maintenance of sympatric genome diversity in B. burgdorferi without adaptive divergence. We suggest that pervasive recombination makes it less likely for local B. burgdorferi genomic groups to achieve host specialization. B. burgdorferi genomic groups in the northeastern United States are thus best viewed as constituting a single bacterial species, whose generalist nature is a key to its rapid spread and human virulence. G ENETIC discontinuity, the basis of biodiversity, is ubiquitous in prokaryotes as well as in eukaryotes. Most bacterial populations display a highly clonal genetic structure, in which the observable number of multilocus genotypes is far fewer than the number expected under the assumption of free recombination (Maynard Smith et al. 1993). Bacterial clonality was originally thought of as a result of a lack or rarity of recombination among asexually reproducing and independently evolving clones (Ochman and Selander 1984). Since then, molecular surveys of natural bacterial populations using protein electrophoresis, multilocus sequencing typing (MLST), and whole-genome PRJNA3, PRJNA28633, PRJNA19839, PRJNA29359, PRJNA28629, PRJNA29357, PRJNA21003, PRJNA19835, PRJNA28627, PRJNA21001, PRJNA29361, PRJNA28621, PRJNA19837, PRJNA20999, PRJNA28631, PRJNA29363, PRJNA17057, PRJNA19841, PRJNA12554, PRJNA28625, PRJNA29573, PRJNA19843, and PRJNA28635. 1 Present address: Odum School of Ecology, University of Georgia, Athens, GA 30602. sequencing revealed that horizontal genetic exchange is in fact often more frequent than point mutations in bacteria, including species known as strongly clonal (Maynard Smith et al. 1993;Feil and Spratt 2001;Didelot and Maiden 2010;Retc...

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“…ClustalW was used to align the carAB large and small subunits for the CO 2 -dependent S. aureus strain from the most identical contig against the same encoding genes from different protein strains [17][18][19]. These strains were S. aureus COL, S. aureus Newman, S. aureus Mu50, S. aureus N315, S. aureus ED98, S. aureus ED133, S. aureus ST398, S. epidermidis ATCC 12228, S. carnosus TM300 and S. saprophyticus ATCC15305.…”

Section: Multiple Sequences Alignment Using Clustalw and Jalviewmentioning

confidence: 99%

Using Different Bioinformatics Software Tools for Determining the Carbon Dioxide (CO2) Dependence in Staphhylococcus aureus

Sa¹,

Alsuhibany²

2015

J Comput Sci Syst Biol

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Keywords: Staphylococcus aureus; CO 2 -dependent S. aureus strains;MUMmer; BLAST; Jalview; ClustalW IntroductionStaphylococcus aureus (S. aureus) is a Gram-positive, immobile and spherically shaped (around 1 μm diameter) bacterium that occurs in microscopic bunches similar to grapes, as shown in Figure 1. In general, S. aureus shows two different colonies; on agar dishes S. aureus forms huge golden yellow colonies, while on blood agar dishes it has haemolytic properties. In addition, S. aureus has the ability to produce the lactic acid as it is considered to be an optional anaerobic, which grows either by aerobic respiration or by fermentation [2].Commonly, S. aureus can be found on the skin, like part of the regular flora and in the respiratory tract of the human. Furthermore, this bacterium can be found as skin lesions or impetigo in the adult individual as an abscess in children or as mastitis in cattle [3,4]. It has been recorded that, around 20% of the populations are considered to have a long-term case of S. aureus. Moreover, there are different diseases that can be caused by S. aureus such as soft tissue infections, life-threatening septicaemia, superficial skin, endocarditis and toxic shock syndrome [5]. In most cases β-lactam antibiotics, clindamycin, tetracycline and sulpha drugs are using as treatments for the S. aureus infections. In the past, before introducing penicillin as a treatment in 1949, the major cause of mortality in patients was the hospital-acquired (nosocomial) infections, which are caused by S. aureus. After that, the penicillin-resistant S. aureus isolates were first discovered in hospitals. Then the first discovery of the Methicillin-resistant nosocomial S. aureus isolates was in 1961 [6]. Afterwards, in hospitals and intensive care units the Methicillin-resistant S. aureus (MRSA) became common worldwide. Nowadays, more than 30% of the bacterial nosocomial infections occurring in intensive care units are caused by MRSA. Previously, MRSA was confined only to hospitals and then new strains of MRSA arose in the community causing different infections in healthy humans. In the 1990s, an extreme Community-Acquired Methicillinresistant S. aureus (CA-MRSA) strain was discovered in Australia [7]. Normally, CA-MRSA has the ability to cause different infections such as a spontaneous abscess either on the skin or on the soft-tissues. In addition, the CA-MRSA strains can be spread quickly in a community, and can affect children and healthy individuals.Pinto and Merlino found that the CO2-dependent S. aureus was detected for the first time in 1955 [8]. These organisms can be found as an inhabitant of small colony variant (SCV) S. aureus, which can cause recurrent and persistent infections. In addition, SCV S. aureus AbstractStaphylococcus aureus (S. aureus) is a Gram-positive bacterium that occurs in microscopic bunches similar to grapes. In general, S. aureus shows two different colonies; on agar dishes S. aureus forms huge golden yellow colonies, while on blood agar dishes it has haemolytic prop...

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ClustalW-MPI: ClustalW analysis using distributed and parallel computing

Cited by 409 publications

References 6 publications

High aromatic ring-cleavage diversity in birch rhizosphere: PAH treatment-specific changes of I.E.3 group extradiol dioxygenases and 16S rRNA bacterial communities in soil

High aromatic ring-cleavage diversity in birch rhizosphere: PAH treatment-specific changes of I.E.3 group extradiol dioxygenases and 16S rRNA bacterial communities in soil

Pervasive Recombination and Sympatric Genome Diversification Driven by Frequency-Dependent Selection in Borrelia burgdorferi, the Lyme Disease Bacterium

Using Different Bioinformatics Software Tools for Determining the Carbon Dioxide (CO2) Dependence in Staphhylococcus aureus

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