Biology Reference
In-Depth Information
that T-Coffee performances will depend on the nature and size of
your data (
see Note 3
).
1. M-Coffee
M-Coffee [
9
] is a meta-method meant to combine the output
of several alternative aligners into one final output, assuming
that errors produced by independent prediction systems should
not be consistent, therefore suggesting agreement as an indica-
tion of correctness. M-Coffee alignments are on overall less
accurate than T-Coffee alignments; however they reveal incon-
sistent regions of your alignments. M-Coffee is run using the
following command line:
t_coffee -seq sh3.fasta -mode mcoffee
By default, M-Coffee runs eight different aligners; however
the users have the option to generate their own combination.
The list of all alternative aligners available in the T-Coffee
package can be displayed by simply running the command
t_coffee
. One of the most used variants is defined as Fast M-
Coffee (fmcoffee), combining the current three fastest aligners
(kalign, mafft, and muscle). Fast M-Coffee (Fig.
1b
)isrun
using the following command line:
t_coffee -seq sh3.fasta -mode fmcoffee
2. PSI-Coffee
PSI-Coffee [
8
,
10
] is designed for aligning distantly related
proteins using evolutionary information by combining homol-
ogy extension and T-Coffee consistency-based progressive align-
ment. Homology extension consists in generating a homology
profile by running a BLAST against nr for each sequence within
a given dataset (
see Note 4
). These profiles are then aligned
rather than their corresponding sequences within the given
dataset. PSI-Coffee is slower than T-Coffee or M-Coffee
(Table
1
), but it is the most accurate mode of T-Coffee using
only sequence information. PSI-Coffee (Fig.
1c
) is run using the
following command:
t_coffee -seq sh3.fasta -mode psicoffee
A particular application of PSI-Coffee is TM-Coffee [
10
],
a mode especially designed for transmembrane protein (TMP) in
which the homology extension step uses a nonredundant database
containing only TMP sequences. TM-Coffee achieves the same
level of accuracy as PSI-Coffee while only requiring a tenth of the
CPU time. TM-Coffee is run using the following command:
t_coffee -seq sh3.fasta -mode psicoffee -template_file
PSITM
The PSITM template file is automatically generated and is
used to display a colored MSA version (.tm_html output file)
