Python for Bioinformatics

13 Gapped Alignments

In Chapter 8 sequences were aligned using dynamic programming and in Chapter 12 an assembly was created using nongapped alignments. This chapter will combine the two approaches to create an assembly of gapped alignments. The procedures presented here follow the logic of programs such as CLUSTALW (Thompson, 1999).

13.1 Theory of Gapped Alignments

When considering multiple sequence alignments with gapped sequences, there is an added level of complexity. Consider the alignments of ABCE, ACDE, and AABE. Aligning the first two sequences would create the contig [ABC-E, A-CDE]. Aligning the first and third sequences provides [A-BCE, AAB-E]. Both are valid alignments and both contigs include the first sequence. The two contigs can ...