Editing Sequence alignment (section)

===Motif finding===
Motif finding, also known as profile analysis, constructs global multiple sequence alignments that attempt to align short conserved [[sequence motif]]s among the sequences in the query set. This is usually done by first constructing a general global multiple sequence alignment, after which the highly [[conservation (genetics)|conserved]] regions are isolated and used to construct a set of profile matrices. The profile matrix for each conserved region is arranged like a scoring matrix but its frequency counts for each amino acid or nucleotide at each position are derived from the conserved region's character distribution rather than from a more general empirical distribution. The profile matrices are then used to search other sequences for occurrences of the motif they characterize. In cases where the original [[data set]] contained a small number of sequences, or only highly related sequences, [[pseudocount]]s are added to normalize the character distributions represented in the motif.