
180 R Programming for Bioinformatics
different tasks, such as motif finding, aligning multiple sequences, aligning
genes, aligning genomes, local versus global alignments, and all often require
slightly different tools. The tools currently available in Bioconductor are lim-
ited and currently only support pairwise global alignment. There are two
basic types of algorithms that are widely used: optimal alignment that typ-
ically relies on dynamic programming and heuristic alignments that do not
necessarily provide an optimal solution but are fast and allow users to work
on large problems.
Two, possibly related, biological sequences can differ in a number