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 http://ibivu.cs.vu.nl/programs/pralinewww/.

Figure 1

The PRALINE results page headers. A: The subtitle indicating which iteration results are presented on this page (only available if iteration >0 is selected). B: The time taken to run the job and statistics related to the visible alignment. C: The links to all other available iteration cycle results (only available if iteration >0 is selected). D: The link to download all job files as a compressed file. E: Links to tabulated specific file types. F: Links to iteration-specific output files (only available if iteration >0 is selected). G: The button that hides/reveals the profile pre-processing scores of the sequence set (only available if profile pre-processing is selected). H: The buttons that switch between colour schemes. I: The button that generates and opens a PDF version of the alignment in the visible colour scheme.

Figure 2

The PRALINE_PSI P450 alignment using both PROFsec and DSSP secondary structure integration settings. The alignment has been sectioned to focus on the regions containing the conserved motifs of the cytochrome P450 enzymes (signified by the black bars above the rulers). (A) The oxygen-binding motif, (B) the ExxR motif and (C) the haem-binding motif. For each section, the top colour scheme shows conservation levels according to the colour key and the bottom one shows the secondary structure each residue belongs to (red: helix; green: strand; and clear: coil). The ruler on top of each alignment block shows which parts of the alignment are visible.