Alignment of sequences
- As you can see in the figure below, an alignment tries to match two sequences, adding empty characters or enabling local mismatches.
- The resulting alignment depends on the definition used to compute it. For example, one can assume that adding a empty character or enabling a mismatch has a cost of one and that the best alignment is the one with the lowest score.
132955 ATGATGAACAGACGTCATTTTATTCAA---ATTAGTGCGACCAGTATTCTTGCATTAAGT
::: ::: ::: : : ::: ::: ::: : ::: :: : :
_ ATG---------CGTTGTTTAGCACTAGATATTGGTGGGACAAAAATTGCAGCGGCGATT
132955 GCAAAC-----CG---TTTTGCGATG---GCAAAAGGAAAGAGCG-------ATGTTGAT
: ::: :: :: :: : : ::::: : : : : :::: : :
_ GTAAAAAATGGCGAAATTGAGCAACGTCAGCAAATTCATACACCACGTGAAAATGTCG-T