Blastmultal, a Blast Extension for Similarity Searching with Alignment Graphs Blastmultal, a Blast Extension for Similarity Searching with Alignment Graphs Blastmultal, a Blast Extension for Similarity Searching with Alignment Graphs

We describe a new method of processing similarity queries of a proteic multiple alignment with a set (database) of protein sequences, or similarity queries of a protein sequence with a set of protein alignments. We use a representation of multiple alignments as alignment-graphs. Comparisons with diierent classical methods is made. This new method allows the detection of subtle similarities which are not found by the other methods. It has direct applications for similarities querying with the database of protein domains ProDom. BlastMultAl: une extension de Blast pour la recherche de similarit es au moyen de graphes d'alignement. R esum e. Nous d ecrivons une nouvelle m ethode de recherche de similarit es d'un alignement multiple de prot eines avec un ensemble (une base de donn ees) de s equences prot eiques, ou de recherche de similarit es d'une s equence prot eique avec un ensemble d'alignements multiples de prot eines. Nous comparons cette approche avec des approches classiques. Cette nouvelle m ethode permet la d etection de similarit es subtiles qui ne sont pas mises en evidence par les autres m ethodes; elle a des applications directes pour eeectuer des recherches de similarit es avec la base de domaines prot eiques ProDom. Abstract We describe a new method of processing similarity queries of a proteic multiple alignment with a set (database) of protein sequences, or similarity queries of a protein sequence with a set of protein alignments. We use a representation of multiple alignments as alignment-graphs. Comparisons with diierent classical methods is made. This new method allows the detection of subtle similarities which are not found by the other methods. It has direct applications for similarities querying with the database of protein domains ProDom.