Biology Reference
In-Depth Information
T-Coffee accepts as input virtually any type of sequences, nucleic
acid or amino acid, given in a standard format (fasta or ClustalW
only). You must have your sequence ready in order to use T-Coffee;
however T-Coffee package comes along with reformatting options
allowing you to change the format or manipulate your input
sequences (cf. T-Coffee Tutorial at http://www.tcoffee.org/
Projects/tcoffee/ ) .
A few external tools or databases are required for specific
T-Coffee modes (BLAST, PDB, nr) and are, by default, accessed
via their respective servers. T-Coffee can use instead versions
installed locally; however their installation and management are
the user responsibility.
2.4
Input Information
3 Methods
T-Coffee in its default mode runs on all types of sequences you
provide (nucleic acids or amino acids). For all methods described
here, T-Coffee always generate the following output files:
- The resulting alignment (you can choose your format for the
output MSA using the flag -output).
- The resulting guide tree (tree generated to build the alignment;
it is not a phylogenetic tree).
- An html file that can be visualized using any browser, showing
the resulting alignment colored according to the T-Coffee color
scheme. The color scheme is related to the consistency from blue
(low-consistency regions) to red (high-consistency regions).
Depending on your biological problem and/or the nature of
your sequences, you may choose a more adapted mode of T-Coffee
rather than the default mode ( see Note 2 ). For each case, additional
output file will be detailed in each section.
The different T-Coffee modes were used to aligned proteins of the
sh3 protein domain family as an example. All alignments generated
here are shown in Fig. 1 and compared to a reference alignment
manually curated to evaluate their respective accuracy, shown in
Table 1 . The CPU time requirement for each mode is indicated also
in Table 1 . While using T-Coffee on your own dataset, keep in mind
3.1 Aligning Protein
Sequences
Fig. 1 (continued) blue-gray: aromatic and polar motifs of the RT loop, respectively; beige: conserved triad in
the binding pocket. Asterisks indicate conserved amino acid in all sequences. Colons indicate position of the
MSA composed of residues with similar physicochemical properties. Dots indicate columns of the MSA for
which semi-conserved substitutions are observed. (a-d) MSA of the sh3 sequences with the T-Coffee default
mode, fast M-Coffee, PSI-Coffee, and Expresso, respectively. The alignments are colored according to their
consistency (CORE index). Regions in red have the highest consistency whereas regions in blue have the
lowest consistency (see step 1 in Subheading 3.3 ). Functional motifs correctly aligned or misaligned are
tagged with the word “OK” or “NO,” respectively
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