T-coffee

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T-coffee
Basic data

Current  version 8.99
(January 25, 2011 )
operating system UNIX , Linux , MS-Windows
programming language C.
category Bioinformatics software
License GPL
http://www.tcoffee.org/

T-Coffee ( T ree-based C onsistency O bjective F unction F or alignment E valuation) is a program in the field of bioinformatics . It is used to create a multiple sequence alignment . The program takes a progressive approach. It generates a collection of pairwise alignments that lead to the multiple sequence alignment. It can also combine pre-calculated alignments and use structure information from PDB files (3D coffee). It includes features to evaluate the quality of alignments and a certain ability to identify motifs (mocha). Alignments are output in the ALN format ( Clustal ) by default , but various other formats can also be used, such as PIR, MSF and FASTA. The most common input formats ( FASTA , PIR ) are also supported.

Compared to other alignment programs

Although the standard output format is similar to ClustalW, there are enough differences from the ClustalW / X format that many programs that support the Clustal format cannot use it. The original ClustalW format can be -output=clustalw_alnoutput using the " " option .

An important characteristic of T-Coffee is its ability to combine different methods and data types. In the current version, T-Coffee can combine structures and sequences of proteins as well as RNAs. It can also combine the output of various commonly used sequence and structural alignment programs into a single alignment.

T-Coffee also includes a "seq_reformat" reformat tool. Detailed documentation is available on the T-Coffee website. There is also a tutorial.

Variations

M-Coffee

M-Coffee is a special mode from T-Coffee that makes it possible to combine the output of different multiple-sequence alignment packages (Muscle, ClustalW, Mafft, ProbCons etc.). The resulting alignments are slightly better than the individual ones. However, it is more important that the program marks the regions in the alignment in which the various individual programs match. Regions with a high agreement are generally better aligned.

Expresso and 3D coffee

These special modes from T-Coffee enable the connection of sequence and structure in an alignment. The structure-based alignments can be created with the help of the most common structure alignment programs (e.g. TMalign, Mustang and sap).

R-Coffee

R-Coffee is a special mode of T-Coffee that enables RNA sequences to be aligned using secondary structures.

Web links

Individual evidence

  1. ↑ github.com . (accessed on September 18, 2019).
  2. ↑ C. Notredame, DG Higgins, J. Heringa: T-Coffee: A novel method for fast and accurate multiple sequence alignment . In: J Mol Biol. Volume 302 , no. 1 , September 8, 2000, pp. 205-217 , doi : 10.1006 / jmbi.2000.4042 , PMID 10964570 .
  3. ↑ A complete list