Improving your target-template alignment with MODalign

Abstract

Summary: MODalign is an interactive web-based tool aimed at helping protein structure modelers to inspect and manually modify the alignment between the sequences of a target protein and of its template(s). It interactively computes, displays and, upon modification of the target-template alignment, updates the multiple sequence alignments of the two protein families, their conservation score, secondary structure and solvent accessibility values, and local quality scores of the implied three-dimensional model(s). Although it has been designed to simplify the target-template alignment step in modeling, it is suitable for all cases where a sequence alignment needs to be inspected in the context of other biological information.

Availability and implementation: Freely available on the web at http://modorama.biocomputing.it/modalign. Website implemented in HTML and JavaScript with all major browsers supported.

Contact: jan.kosinski@uniroma1.it.

Fig. 1.

The MODalign result page. The alignment can be edited in the target-template alignment section. When the alignment is modified, the output, such as coloring by sequence conservation or highlighting of potential errors, is modified in real time, while QMEAN can be recalculated on request.