T-Coffee
Encyclopedia
T-Coffee is a multiple sequence alignment
software using a progressive approach. It generates a library of pairwise alignments to guide the multiple sequence alignment. It can also combine multiple sequences alignments obtained previously and in the latest versions can use structural information from PDB
files (3D-Coffee). It has advanced features to evaluate the quality of the alignments and some capacity for identifying occurrence of motifs (Mocca). It produces alignment in the aln format (Clustal
) by default, but can also produce PIR, MSF and FASTA format. The most common input formats are supported (FASTA
, PIR
).
An important specificity of T-Coffee is its ability to combine different methods and different data types. In its latest version, T-Coffee can be used to combine protein sequences and structures, RNA sequences and structures. It can also run and combine the output of the most common sequence and structure alignment packages. For a complete list see: tclinkdb.txt
T-Coffee comes along with a sophisticated sequence reformatting utility named seq_reformat. An extensive documentation is available from t_coffee_technical.htm along with a tutorial t_coffee_tutorial.htm
Multiple sequence alignment
A multiple sequence alignment is a sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a lineage and are descended from a common ancestor...
software using a progressive approach. It generates a library of pairwise alignments to guide the multiple sequence alignment. It can also combine multiple sequences alignments obtained previously and in the latest versions can use structural information from PDB
Protein Data Bank
The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....
files (3D-Coffee). It has advanced features to evaluate the quality of the alignments and some capacity for identifying occurrence of motifs (Mocca). It produces alignment in the aln format (Clustal
Clustal
Clustal is a widely used multiple sequence alignment computer program. The latest version is 2.1. There are two main variations:*ClustalW: command line interface*ClustalX: This version has a graphical user interface...
) by default, but can also produce PIR, MSF and FASTA format. The most common input formats are supported (FASTA
FASTA
FASTA is a DNA and protein sequence alignment software package first described by David J. Lipman and William R. Pearson in 1985. Its legacy is the FASTA format which is now ubiquitous in bioinformatics.- History :...
, PIR
Protein Information Resource
The Protein Information Resource , located at Georgetown University Medical Center , is an integrated public bioinformatics resource to support genomic and proteomic research, and scientific studies-History:...
).
Comparisons with other alignment software
While the default output is a Clustal-like format, it is sufficiently different from the output of ClustalW/X that many programs supporting Clustal format cannot read it; fortunately ClustalX can import T-Coffee output so the simplest fix for this issue is usually to import T-Coffee's output into ClustalX and then re-export. Another possibility is to request the strict Clustalw output format with the option "-output=clustalw_aln".An important specificity of T-Coffee is its ability to combine different methods and different data types. In its latest version, T-Coffee can be used to combine protein sequences and structures, RNA sequences and structures. It can also run and combine the output of the most common sequence and structure alignment packages. For a complete list see: tclinkdb.txt
T-Coffee comes along with a sophisticated sequence reformatting utility named seq_reformat. An extensive documentation is available from t_coffee_technical.htm along with a tutorial t_coffee_tutorial.htm
M-Coffee
M-Coffee is a special mode of T-Coffee that makes it possible to combine the output of the most common multiple sequence alignment packages (Muscle, ClustalW, Mafft, ProbCons, etc.). The resulting alignments are slightly better than the individual one, but most important the program indicates the alignment regions where the various packages agree upon. Regions of high agreement are usually well aligned.Expresso and 3D-Coffee
These are special modes of T-Coffee making it possible to combine sequence and structures in an alignment. The structure based alignments can be carried out using the most common structural aligners such as TMalign, Mustang, and sap.R-Coffee
R-Coffee is a special mode of T-Coffee making it possible to align RNA sequences while using secondary structure information.See also
- List of sequence alignment software
- ClustalClustalClustal is a widely used multiple sequence alignment computer program. The latest version is 2.1. There are two main variations:*ClustalW: command line interface*ClustalX: This version has a graphical user interface...
- MAFFTMAFFTMAFFT is a multiple sequence alignment program for amino acid or nucleotide sequences. MAFFT is freely available for academic use, without any warranty.- External links :* * * at EBI* at GenomeNet* in MyHits, SIB...
- LiSA Web — a library of open source structural analysis algorithms.
- MARNA — a server for multiple alignment of RNARNARibonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
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