Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee

Abstract

Expresso is a multiple sequence alignment server that aligns sequences using structural information. The user only needs to provide sequences. The server runs BLAST to identify close homologues of the sequences within the PDB database. These PDB structures are used as templates to guide the alignment of the original sequences using structure-based sequence alignment methods like SAP or Fugue. The final result is a multiple sequence alignment of the original sequences based on the structural information of the templates. An advanced mode makes it possible to either upload private structures or specify which PDB templates should be used to model each sequence. Providing the suitable structural information is available, Expresso delivers sequence alignments with accuracy comparable with structure-based alignments. The server is available on .

Reaction mechanism of azoreductases suggests convergent evolution with quinone oxidoreductases

“…Phylogenetic tree showing the evolution of a group of 20 two flavodoxin enzymes. The dendrogram was generated via the neighbor-joining method as part of the Expresso multiple sequence alignment algorithm (Armougom et al, 2006). Bacterial azoreductases are highlighted boxed in blue, heavy metal reductases are boxed in green and mammalian NQO related enzymes are boxed in red.…”

“…A phylogenetic tree has been generated using the neighborjoining method for the amino acid sequence of flavodoxin like proteins (Fig. 8) (Armougom et al, 2006). This tree clearly shows the division of the enzymes into three groups: bacterial azoreductases, enzymes that are related to the mammalian NQO enzymes and heavy metal reducing enzymes.…”

Potassium Ion Channels: Could They Have Evolved from Viruses?

“…Therefore, we used structural information to guide us in the construction of the multiple alignment of K + channels using the 3D-Coffee/Expresso program (Armougom et al, 2006). The 3D-Coffee alignment was further corrected manually, and poorly aligned regions outside the selectivity filter and pore helix were discarded.…”

A novel classification system to predict the pathogenic effects of CHD7 missense variants in CHARGE syndrome

“…This indicates that sufficiently accurate models can be constructed of the conserved regions and that the location of many of the CHD7 variants can be predicted with reasonable accuracy. Multiple sequence alignments and structural alignments of the CHD7 target structure and the template structures were performed using Expresso/T-Coffee [Armougom et al, 2006;Notredame et al, 2000]. The homology models of the CHD7 protein were constructed using YASARA Structure version 11.4.18 using standard settings.…”