The Blocks Searcher Tool

For searching a database of blocks, the first position of the sequence is aligned with the first position of the first block, and a score for that amino acid is obtained from the profile column corresponding to that position. Scores are summed over the width of the alignment, and then the block is aligned with the next position.
This procedure is carried out exhaustively for all positions of the sequence for all blocks in the database, and the best alignments between a sequence and entries in the Blocks database are reported. The score of the block is designed to indicate how well does the query sequence represent the block group. Typically, a group of proteins has more than one region in common and their relationship is represented as a series of blocks separated by unaligned regions. Naturally, more high scoring blocks strong then the hypothesis that the query and the groups are related.