MULTICLUSTAL: a systematic method for surveying Clustal W alignment parameters.

Yuan, Jeffrey; Amend, A.; Borkowski, Janusz; DeMarco, Robert; Bailey, Warren; Liu, Yuan; Xie, Guochun; Blevins, Richard

doi:10.1093/bioinformatics/15.10.862

Cited by 39 publications

(18 citation statements)

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“…This search method eliminates any biases or errors due to incomplete or improper sequence annotation. Homologous protein sequences were aligned using MultiClustal (Yuan et al 1999), which runs iterative ClustalW alignments in order to identify the optimal alignment parameters. In many cases, final multiple sequence alignments were adjusted manually.…”

Section: Methodsmentioning

confidence: 99%

Proposed Guidelines for a Unified Nomenclature and Phylogenetic Analysis of Type III Hop Effector Proteins in the Plant Pathogen Pseudomonas syringae

Lindeberg¹,

Stavrinides²,

Chang³

et al. 2005

MPMI

133

103

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Pathovars of Pseudomonas syringae interact with their plant hosts via the action of Hrp outer protein (Hop) effector proteins, injected into plant cells by the type III secretion system (TTSS). Recent availability of complete genome sequences for a number of P. syringae pathovars has led to a significant increase in the rate of effector discovery. However, lack of a systematic nomenclature has resulted in multiple names being assigned to the same Hop, unrelated Hops designated by the same alphabetic character, and failure of name choices to reflect consistent standards of experimental confirmation or phylogenetic relatedness. Therefore, specific experimental and bioinformatic criteria are proposed for proteins to be designated as Hops. A generic Hop name structure, HopXY#pv strain, also is proposed, wherein family membership is indicated by the alphabetic characters, subgroup membership numerically, and source pathovar and strain in subscript. Guidelines are provided for phylogenetic characterization and name selection for Hops that are novel, related to previously characterized Hops, chimeras, pseudogenes, truncations, or nonexpressed alleles. Phylogenetic analyses of previously characterized Hops are described, the results of which have been used to guide their integration into the proposed nomenclature.

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Section: Methodsmentioning

confidence: 99%

Proposed Guidelines for a Unified Nomenclature and Phylogenetic Analysis of Type III Hop Effector Proteins in the Plant Pathogen Pseudomonas syringae

Lindeberg¹,

Stavrinides²,

Chang³

et al. 2005

MPMI

133

103

View full text Add to dashboard Cite

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“…Sequences were aligned using the modified ClustalW algorithm MultiClustal (22). The resulting alignment was shaded using Genedoc (available at www.cris.com/ϳketchup/genedoc.shtml) and Adobe Illustrator.…”

Section: Methodsmentioning

confidence: 99%

Purification and Molecular Characterization of cGMP-dependent Protein Kinase from Apicomplexan Parasites

Gurnett¹,

Liberator²,

Dulski³

et al. 2002

Journal of Biological Chemistry

161

168

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“…Longer gaps are also known to be rare as compared with shorter ones, so alignments containing long gaps are favored less (Waterman et al 1976;Gu and Li 1995;Qian and Goldstein 2001;Miklos et al 2004). However, the exact value to be assigned to each parameter is difficult to determine, as it is expected to differ between closely and distantly related species and vary from species to species (Vingron and Waterman 1994;Wheeler 1995;Zhu et al 1998;Yuan et al 1999). Although progress has been made in establishing biological justification for the use of some scoring schemes, a comprehensive theoretical framework for gap and substitution penalties still eludes us (Gu and Li 1995;Miklos et al 2004).…”

Section: Practical Sequence Alignmentmentioning

confidence: 99%

Multiple sequence alignment: In pursuit of homologous DNA positions

2007

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DNA sequence alignment is a prerequisite to virtually all comparative genomic analyses, including the identification of conserved sequence motifs, estimation of evolutionary divergence between sequences, and inference of historical relationships among genes and species. While it is mere common sense that inaccuracies in multiple sequence alignments can have detrimental effects on downstream analyses, it is important to know the extent to which the inferences drawn from these alignments are robust to errors and biases inherent in all sequence alignments. A survey of investigations into strengths and weaknesses of sequence alignments reveals, as expected, that alignment quality is generally poor for two distantly related sequences and can often be improved by adding additional sequences as stepping stones between distantly related species. Errors in sequence alignment are also found to have a significant negative effect on subsequent inference of sequence divergence, phylogenetic trees, and conserved motifs. However, our understanding of alignment biases remains rudimentary, and sequence alignment procedures continue to be used somewhat like benign formatting operations to make sequences equal in length. Because of the central role these alignments now play in our endeavors to establish the tree of life and to identify important parts of genomes through evolutionary functional genomics, we see a need for increased community effort to investigate influences of alignment bias on the accuracy of large-scale comparative genomics.The relative positions of nucleotides within the same gene in different species and in duplicated genomic regions are disturbed by insertion and deletion of stretches of DNA over evolutionary time. This leads to differences in the length of the homologous regions in the genome, with more distant relatives having a higher likelihood of sequence length difference. A comparison of lengths of genome segments spanning protein-coding genes in human and mouse shows the extent of the effect of evolution by insertions and deletions (Fig. 1). The lengths of noncoding orthologous sequences have also evolved substantially after divergence over 90 million years ago. A grand challenge in comparative genomics is to line up these bases by inserting gaps in sequences, because genomic analyses must be based on comparisons between bases at positions (sites) that coincided in a common ancestor. The task is to re-establish (estimate) the ancestral site-wise homology obfuscated by the insertiondeletion and substitution processes. Naturally, this operation has come to be known as "alignment," and the resulting set of sequences, all of which are the same length (taking gaps in to account), is also called an alignment (Fig. 2). We can distinguish between "pairwise" alignments, in which sequences, even if they are part of a larger set, are aligned only in pairs, and "multiple" alignments, in which more than two sequences are aligned simultaneously.Alignment procedures may also be classified as either "global" or "local...

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MULTICLUSTAL: a systematic method for surveying Clustal W alignment parameters.

Abstract: MULTICLUSTAL is a Perl script designed to automate the process of alignment parameter choice for Clustal W with the goal of generating high quality multiple sequence alignments.

Cited by 39 publications

References 0 publications

Proposed Guidelines for a Unified Nomenclature and Phylogenetic Analysis of Type III Hop Effector Proteins in the Plant Pathogen Pseudomonas syringae

Proposed Guidelines for a Unified Nomenclature and Phylogenetic Analysis of Type III Hop Effector Proteins in the Plant Pathogen Pseudomonas syringae

Purification and Molecular Characterization of cGMP-dependent Protein Kinase from Apicomplexan Parasites

Multiple sequence alignment: In pursuit of homologous DNA positions

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