PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information

Abstract

PRofile ALIgNEment (PRALINE) is a fully customizable multiple sequence alignment application. In addition to a number of available alignment strategies, PRALINE can integrate information from database homology searches to generate a homology-extended multiple alignment. PRALINE also provides a choice of seven different secondary structure prediction programs that can be used individually or in combination as a consensus for integrating structural information into the alignment process. The program can be used through two separate interfaces: one has been designed to cater to more advanced needs of researchers in the field, and the other for standard construction of high confidence alignments. The web-based output is designed to facilitate the comprehensive visualization of the generated alignments by means of five default colour schemes based on: residue type, position conservation, position reliability, residue hydrophobicity and secondary structure, depending on the options set. A user can also define a custom colour scheme by selecting which colour will represent one or more amino acids in the alignment. All generated alignments are also made available in the PDF format for easy figure generation for publications. The grouping of sequences, on which the alignment is based, can also be visualized as a dendrogram. PRALINE is available at .

Structural Insight into the Mechanism of Activation of the Toll Receptor by the Dimeric Ligand Spätzle

“…The structure templates for the target proteins used for homology modeling were searched using a profile hidden Markov modelbased algorithm HHPRED (16) and a threading algorithm Sparks (17). The statistically most significant alignments from both methods were evaluated and used as basis for rigorous pairwise sequence alignment with the aid of a profile-based approach using PRALINE (18) and manual refinement.…”

Evidence of Distinct Channel Conformations and Substrate Binding Affinities for the Mitochondrial Outer Membrane Protein Translocase Pore Tom40

“…Linear sequence alignments and conservation comparisons were generated utilizing PRALINE (25) and Clustal W (26) servers. Secondary structure predictions were made using a combination of the PRALINE and PSIPRED (27) servers.…”

“…Fungal Tom40 alignments and secondary structure predictions. Tom40 sequences from S. cerevisiae, N. crassa, and C. glabrata were analyzed for sequence conservation and secondary structure prediction using a combination of the PRALINE alignment toolbox (25), ClustalW (26), and the PSIPRED protein structure prediction server (27). Consensus symbols below the alignment indicate either a fully conserved residue (*), a conservation of strongly similar residues (:), or a conservation of weakly similar residues (.).…”

Three-dimensional structure of a schistosome serpin revealing an unusual configuration of the helical subdomain

“…A raw alignment of serpin sequences was generated by the PRALINE server (Simossis & Heringa, 2005) incorporating secondary-structure prediction by PSIPRED (Jones, 1999). This alignment was adjusted manually using the X-ray structures of human antithrombin III (ATIII) and ShSPI (PDB entries 1e05 and 3sto, respectively; McCoy et al, 2003).…”