Biology Reference
In-Depth Information
Table 1
Comparisons between a manually curated alignment of eight sh3 domains
and the different alignment generated with the different T-Coffee modes.
CPU times are given for alignments computed with an 8 Intel(R) Xeon(R)
CPU E5504 at 2.00 GHz
Method
Column score (CS)
CPU time (s)
T-Coffee
69.8
0.5
Fast M-Coffee
74.7
0.8
PSI-Coffee
80.0
21.7
Expresso
90.0
32.6
reflecting structural predictions (yellow: inside loop; red: TM
helix; blue: outside loop).
3. Expresso/3D-Coffee
Expresso/3D-Coffee [ 11 , 12 ] is a multiple structural aligner,
using the 3D structures available in the Protein Data Bank
(PDB) as templates to align the sequences within a given
dataset. It is suited when all the sequences in the dataset have
a close homolog with a known 3D structure ( see Note 5 ).
Expresso is similar to 3D-Coffee except that template file
and the PDB files are automatically generated and fetched
( see Note 4 ). If no template can be identified for a given
sequence, alignment for this sequence will be achieved using
the default T-Coffee mode. Expresso has been shown to be the
most accurate aligner existing; however it is also the slowest
(Table 1 ). Expresso (Fig. 1d ) is run using the following com-
mand:
t_coffee -seq sh3.fasta -mode expresso
Expresso generates a template file in which the 3D struc-
tures associated with your query sequences are explicitly
declared ( see Note 6 ). The Expresso mode also comes along
several filtering parameters related to the type of 3D structure
(XRAY/NMR), the coverage and the identity between your
query sequences and the identified templates. By default the
structural aligner used is SAP; however the user can freely
choose or combine other structural aligners using the tag -
method. For instance the following command line will fetch
3D structures (ā€œdā€ standing for XRAY and/or ā€œnā€ standing for
NMR) 95 % identical with your query sequences and will align
them using the MUSTANG structural aligner:
t_coffee -seq sh3.fasta -mode expresso -method mustang_
pair -pdb_type dn -pdb_min_sim 95
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