Expresso is the latest T-Coffee mode. The principle of Expresso is simple: the server runs a BLAST between every sequence in your query against the PDB database. If it finds a structure similar enough to a sequence in your dataset (>60% identity), it will use that structure as a template for your sequence.

Installed Expresso

We have currently installed version 5.0.3 of the T_coffee.
The reference for this tool is:

Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee. Armougom F, Moretti S, Poirot O,Audic S, Dumas P, Schaeli B, Keduas V, Notredame C. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W604-8.

The official T_coffee web page is available at this link.

Templates

Template files look something like:

>sp|P08246|ELNE_HUMAN _P_ 1PPGE >sp|P20160|CAP7_HUMAN _P_ 1AE5 >sp|P00757|KLKB4_MOUSE _P_ 1SGFX >sp|Q6H321|KLK2_HORSE _P_ 1GVZA >sp|P00773|ELA1_RAT _P_ 2D26C >sp|Q00871|CTRB1_PENVA _P_ 1AZZB >sp|P21844|MCPT5_MOUSE _P_ 1NN6A >sp|O35205|GRAK_MOUSE _P_ 1MZDA >sp|P07338|CTRB1_RAT _P_ 2CGAB >sp|P80015|CAP7_PIG _P_ 1FY3A >sp|P03953|CFAD_MOUSE _P_ 1FDPD >sp|Q7YRZ7|GRAA_BOVIN _P_ 1OP8F >sp|Q06606|GRZ2_RAT _P_ 1EUFA >sp|P08884|GRAE_MOUSE _P_ 1FI8B

In a template file, _P_ indicates that the template is of type structure (P for PDB). Template files can be generated manually or automatically by the Expresso server. Whenever possible t_coffee will then align your sequences using the structural information contained in the templates. If it encounters enough structures (as shown here) it will produce a genuine structure based sequence alignment.

Expresso form

This server computes Structure based Multiple Sequence Alignments. You only need to provide the sequences. The server will automatically fetch the related structures and use them to guide the alignment.

1. Library Computation
   
• Pairwise Methods : Tcoffee computes its alignments by combining a collection of smaller alignments named a Library. In this section you can select the methods you want to combine into the Tcoffee library. You can choose pairwise and multiple sequence alignment methods

modality	fast	Makes a global fasta style pairwise alignment. For proteins, matrix=blosum62mt, gep=-1, gop=-10, ktup=2. For DNA, matrix=idmat (id=10), gep=-1, gop=-20, ktup=5. Each pair of residue is given a score function of the weighting mode defined by -weight.
	slow	Slow_pair : Identical to fast_pair, but does a full dynamic programming, using the myers and miller algorithm. This method is recommended if your sequences are distantly related.
	lalign	produces local alignments
	clustalw	Uses clustalw (default parameters) to align two sequences. Each pair of residue is given a score function of the weighting mode defined by -weight.e

• Structural Alignments:

What you want to do is to build a T-Coffee library where sequences with a known structures are aligned with a structure alignment program (like sap) while the other sequences are aligned using regular T-Coffee methods.
Sap: structure-structure alignments
Fugue: structure-sequence alignments

2. Output
• You can choose the case and the look of results:

Case	upper	upper case for residues
	lower	lower case for residues
Residue Number	ON	print residue number
	OFF
Order	input	output order based on sequences input order
	aligned	output order based on alignment

3. Input files

• STRUCTURE INPUT:

Specify your personal (PDB) structure data sequences.

• PDB STRUCTRE SELECTION:
  

Specify which PDB structure (template) should be associated with which each sequence. if you don't put a template, Expresso automatically fetch the templates for you. If you want to use our templates, please to write the sequence/template association using the following format (specified template superseed the others):

>sequence_name1 _P_ PDBID

>sequence_name2 _P_ PDBID

...

The good news is that you do not need to have PDB installed locally as T-Coffee will automatically fetch the structures directly from RCSB (the home of PDB). Of course, if your dataset only contains structures, your alignment becomes a structural alignment.

• SEQUENCE INPUT:

Put our sequences for Expresso performing

Expresso Tutorials and Technical Notes

Please refer, to the T_coffee home page.
T_coffee Tutorial (HTML) and T_coffee Technical Notes (HTML)