IIBBA   05544
INSTITUTO DE INVESTIGACIONES BIOQUIMICAS DE BUENOS AIRES
Unidad Ejecutora - UE
congresos y reuniones científicas
Título:
MSA2MI: A server to calculate and visualize mutual information in multiple sequence alignments
Autor/es:
FRANCO SIMONETTI; MORTEN NIELSEN; CRISTINA MARINO BUSLE
Lugar:
Oro Verde. Entre Rçios
Reunión:
Congreso; 3er. Congreso Argentino de Bioinformçatica y Biologçia Computacional; 2012
Institución organizadora:
Asociaciçon Argentina de Bioinformatica y Biologia Computacional
Resumen:
BackgroundMultiple Sequence Alignments (MSAs) of homologous proteins carry at least two levels of information. One is given bythe amino acid frequencies observed at each position of the MSA, and the other is given by the relationship between twoor more positions. The first is known as conservation and the second can be studied in terms of co-variation betweenpositions. The extent of the mutual co-evolutionary relationship between two positions in a protein family can beestimated using Mutual Information (MI) [1]. An algorithm was developed for this task by Marino Buslje et al [2] and ishere made publicly available as a web tool.ResultsWe present a web toolkit that allows users to calculate and visualize the MI between residues in an MSA. The webservice was developed using PHP on the server side with Javascript and Flash on the client-side. The pipeline wasimplemented as modules, making addition of new features easy. The main task is to calculate the MI between all pairs ofcolumns in the MSA. The output is displayed as a MI network using Cytoscape Web [3], where each node correspondsto a column in the MSA and edges between nodes represent significant MI values [2] (Figure 1). Several parameters canbe set in order to calculate and present the data. For example, if the structure of the protein is known, structural data canbe displayed by adding the PDB numbering schema to the nodes and distance information for edges (Figure 1). Also,node coloring can be set to match different attributes, such as conservation value (Figure 1). Additionally, by clickingeach node the relative frequency of different amino acids for this position is shown. Results can be downloaded forfurther user manipulation, which include MI and conservation data in raw format and network files to load onCytoscape´s desktop version.ConclusionsThis web toolkit allows the study of protein families through a simple and interactive interface, utilizing sequence baseddata such as conservation, coevolution and amino acid composition and capable of mapping structural data when available.Available at: www.leloir.org.ar/MSA2MI