T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension
By Paolo Di Tommaso, S. Moretti, Ioannis Xenarios, Miquel Orobitg, Alberto Montanyola, Jia-Ming Chang, Jean-François Taly, Cédric Notredame. Nucleic Acids Res., 2011
1,122 citations recorded by the source corpus.
This article introduces a new interface for T-Coffee, a consistency-based multiple sequence alignment program. This interface provides an easy and intuitive access to the most popular functionality of the package. These include the default T-Coffee mode for protein and nucleic acid sequences, the M-Coffee mode that allows combining the output of any other aligners, and template-based modes of T-Coffee that deliver high accuracy alignments while using structural or homology derived templates. These three available template modes are Expresso for the alignment of protein with a known 3D-Structure, R-Coffee to align RNA sequences with conserved secondary structures and PSI-Coffee to accurately align distantly related sequences using homology extension. The new server benefits from recent improvements of the T-Coffee algorithm and can align up to 150 sequences as long as 10 000 residues and is available from both http://www.tcoffee.org and its main mirror http://tcoffee.crg.cat.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/c81dbe59863d83179e4645a6454b6a7977ec7dfd
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Citations in the corpus
- MAFFT-DASH: integrated protein sequence and structural alignment (2019, methodology): “MSA software such as Expresso (8,9) in the TCoffee package and PROMALS3D (10) allow structural information to be incorporated in order to improve accuracy when aligning remote sequence homologs.”
- Structural model of PORCN illuminates disease-associated variants and drug binding sites (2021, methodology): “2, also known as splice isoform D, 461 amino acids), using the T-Coffee homology extension (PSI-coffee) algorithm (Tommaso et al., 2011).”
- Structural and biophysical properties of FopA, a major outer membrane protein of Francisella tularensis (2022, methodology): “Proteins homologous to FopA sequence were identified by BLAST, and multiple sequence alignment was performed using the program M-Coffee (50).”
- VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors (2011, methodology): “The T–coffee package (8) was employed to generate multiple alignment for each homologue group.”
- Activity-enhancing mutations in an E3 ubiquitin ligase identified by high-throughput mutagenesis (2013, methodology): “Di Tommaso P, et al. (2011) T-Coffee: A web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension.”