Multiple sequence alignment with the Clustal series of programs

By H. Sugawara, Tadashi Koike, Rodrigo Lopez, Toby J. Gibson, Desmond G. Higgins, Julie Dawn Thompson. Nucleic Acids Res., 2003

5,174 citations recorded by the source corpus.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/8df59e797d3671b0dc75f2b6c1ca9af9533166cc

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Ecology

In Molecular Biology

Citations in the corpus

Immune pathways and defence mechanisms in honey bees Apis mellifera (2006, methodology): “Amino acid sequence alignments were carried out using GONNET series weight matrices, with the program CLUSTAL_X (Chenna et al., 2003).”
Towards a Genome-Based Taxonomy for Prokaryotes (2005, methodology): “(A and B) A distance and a maximum likelihood tree, respectively, built with the ProtDist and ProML algorithms of the Phylip package (13) using default settings and, as input sequence, the concatenated protein sequences of all 136 core genes aligned with the ClustalW software (6).”
Late Neogene history of the laurel tree (Laurus L., Lauraceae) based on phylogeographical analyses of Mediterranean and Macaronesian populations (2009, positive): “Sequences were aligned using ClustalW 1.83 (Chenna et al., 2003), with further adjustments by visual inspection.”
A benchmark of multiple sequence alignment programs upon structural RNAs (2005, neutral): “7 -p2m_nseq_min 5 Align-m (5) align_m -m RNA2 -s2p_w 3 ClustalW clustalw -type=dna -align [2, 3] ClustalW (qt) clustalw -type=dna -align -quicktree DIALIGN dialign2-2 -n [4–6] DIALIGN (it) dialign2-2 -n -it DIALIGN (o) dialign2-2 -n -o DIALIGN (it,o) dialign2-2 -n -it -o Handel handalign.”
Understanding eukaryotic linear motifs and their role in cell signaling and regulation. (2008, methodology): “On the top, the multiple sequence alignment was calculated with ClustalW (164), where several motifs are unaligned.”
Identification of conserved regions in the plastid genome: implications for DNA barcoding and biological function (2006, positive): “ClustalX alignment software (Chenna et al. 2003) version 1.”
Diversity of human colonic butyrate-producing bacteria revealed by analysis of the butyryl-CoA:acetate CoA-transferase gene. (2010, methodology): “Clone and reference sequences were aligned with ClustalW (Chenna et al., 2003) and trimmed with Jalview (Clamp et al., 2004).”
Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes (2013, methodology): “For the putative RNA methylase gi|311977703, we used CLUSTALW (Chenna et al., 2003) followed by manual curation of the alignment.”
Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development (2008, methodology): “Subsequent clustering of motifs based solely on sequence similarity (as measured using an scoring approach based on that used for Clustal [95]) enabled us to reduce further the number of motifs of interest by consolidating sequences with slight variations.”
The WRKY Gene Family in Rice (Oryza sativa) (2007, positive): “Domain alignment was performed using Clustalw (Chenna et al. 2003).”
Structural determinants of protein evolution are context-sensitive at the residue level. (2009, background): “To assess the evolutionary constraint imposed on a residue by each property, we first identified positions exhibiting a substitution in any of three closely related yeast species.”