Introduction

Context

Protein family analysis becomes more and more easy and difficult in the same time. Easy as more and more information are available for all aspects of protein characterization (structural, functional, environmental) and difficult because these information are heterogenious and deal with several details levels, ranging from very local data like point mutation up to large scale data like domain organization. These information arise from the post genomic era that is characterized by a massive growth of all information available thanks to high throughput technologies like genomic, proteomic, interactomic and transcriptomic. As a consequence, a new member of a protein family is then surrounded by information that can or not be assigned to it. Such data harvesting and assignation has been implemented in the Macsims software [ref] which integrate and propagate heterogenous information in the environment of the multiple sequence alignment of a protein family. A remaining problem resides in the analysis and the visualization of these information for which Ordalie has been developped.

Ordalie

Ordalie (Ordered ALignment Information Explorer) is a tool intended to explore the informational content of a multiple sequence alignment into a two-dimensional hierarchical manner.
The information running along the sequence can be seen from several scales :

large-scale features: domain ordanization, conserved regions,
middle-scale features: low-complexity region, secondary structure
low-scale or local features: post-translational signal, motation position, residue conservation.

An other axis of analysis consists of the different taxa present in the alignment. The study can be achieved at a global level to characterized the whole family being studied through, i.e. motifs, key signature, up to a particular taxa to identify and specify point mutation positions, and also at an intermediary level to study the features giving raise to sub-family, like identification of differentially conserved residues.
Ordalie embed along with alignment rendering windows, tools for sub-family identification, and residue conservation prediction. All analysis can be done in a structural context, as all available features can be mapped and compared on the available structures of the alignment.