The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.

By Julie Dawn Thompson, Toby J. Gibson, F. Plewniak, François Jeanmougin, Desmond G. Higgins. 1997

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Citations in the corpus

Predicting Functional Effect of Human Missense Mutations Using PolyPhen-2 (2013, methodology): “…panels expanded the multiple sequence alignment panel displays a ﬁxed 75-residue wide window surrounding the variant’s position (the column indicated by black frame), with the alignment colored using the ClustalX (Thompson et al., 1997) scheme for all columns above 50% conservation threshold.”
Protein sectors: evolutionary units of three-dimensional structure (2009, methodology): “…SH2, and SH3 families were collected from the NCBI nonredundant database (release 2.2.14, May-07-2006) through iterative PSI-BLAST (Altschul et al., 1997) and aligned with Cn3D (Wang et al., 2000) and ClustalX (Thompson et al., 1997) followed by standard manual adjustment methods (Doolittle, 1996).”
Homology Modeling a Fast Tool for Drug Discovery: Current Perspectives (2012, methodology): “This is implemented in the most widely used programs (ClustalW[36] and ClustalX[37]).”
GbetaL, a positive regulator of the rapamycin-sensitive pathway required for the nutrient-sensitive interaction between raptor and mTOR. (2003, methodology): “81 (Thompson et al., 1997) using the Gonnet series weight matrix.”
Diversity of lactic acid bacteria and yeasts in Airag and Tarag, traditional fermented milk products of Mongolia (2008, methodology): “The alignments were analyzed to construct a phylogenetic tree and to compare similarities among the sequences by the neighbor-joining method of Saitou and Nei (1987) by using Clustal X software version 1.82 ( Thompson et al. 1997 ).”
Covariance of bacterioplankton composition and environmental variables in a temperate delta system (2003, methodology): “…27F and 907R (5’-CCG TCA ATT CCT TTR AGT TT), yielding readable sequences of about 800 bp. Sequences were automatically aligned with ClustalX (Thompson et al. 1997) and phylogenetic trees were constructed with the PHYLIP package (Felsenstein 1989) using Jukes-Cantor evolutionary distances…”
Phylogeny of the American Amaryllidaceae based on nrDNA ITS sequences (2000, methodology): “We also used the program ClustalX (Higgins and Sharp 1988, Thompson et al. 1997) to align the sequences with a gap opening penalties of both 15 and 30 and gap extension penalties of 0.5 to 6.66.”
Patterns and processes in the evolutionary history of parrotfishes (Family Labridae) (2012, methodology): “Duplicate sequences were edited using SEQUE NCHER, version 4.5 (Gene Codes Corp.), automatically aligned using CLUSTALX (Thompson et al., 1997) and finally manually corrected using SE-AL, version 2.0 (http://evolve.zoo.ox.ac.uk) (Rambaut, 1996).”
The Universal Ancestor and the Ancestor of Bacteria Were Hyperthermophiles (2003, methodology): “The protein alignments were constructed using CLUSTALX (Thimpson et al. 1997).”
Complete Genomic Sequence of Human Coronavirus OC43: Molecular Clock Analysis Suggests a Relatively Recent Zoonotic Coronavirus Transmission Event (2005, methodology): “Multiple sequence alignments were prepared by using CLUSTALW (58) and CLUSTALX, version 1.82 ( 59 ) and were manually edited in GENEDOC (46).”
Dark fermentation of xylose and glucose mix using isolated Thermoanaerobacterium thermosaccharolyticum W16 (2008, methodology): “Multiple alignments and calculation of degrees of sequence similarity were performed via Clustal X [22].”