1Methods for alignment of sequences

Accurate alignments of sequences are needed for many types of analyses. Aligned sequences might be the basis of phylogenetic analysis of evolutionary relationships. They are also important for identification of protein functions and for modeling of protein conformation. Alignment methods are also used to search for similarities between new sequences and sequences in databases. Depending on the purposes, different properties of the alignment algorithm are important: searches in extensive databases require speed, while algorithms for alignments of homologous sequences can be optimized to use all available information to produce the most reliable alignment. Alignment algorithms are therefore either global, trying to optimally align entire sequences, or local, finding short segments of high similarity. Scoring matrices All alignment methods need some sort of scoring for matches and mismatches. For a certain alignment, a number is assigned to each position in the sequence depending on the match at that position. The scores for all position in the alignment are then added to calculate a total score, which is used to select the optimal alignment among alternative alignments. Th