In this chapter we’ll explore why determining biological sequence similarity is harder than it might initially seem, and learn about pairwise sequence alignment, the standard approach for determining sequence similarity. On the surface this seems like a pretty straight-forward problem, not one that would have been at the center of decades of research and the subject of one of the most cited papers in modern biology. There are many applications for this, including inferring the biological function of a new protein sequence, the source organism of an observed DNA sequence, and performing molecular phylogenetics to develop hypotheses about the relatedness of organisms. One of the most fundamental problems in bioinformatics is determining how similar a pair of biological sequences are. How long does pairwise sequence alignment take?Ĭomparing implementations of Smith-WatermanĪnalyzing Smith-Waterman run time as a function of sequence lengthĬonclusions on the scalability of pairwise sequence alignment with Smith-Waterman Why this simple procedure is too simplisticĭifferential scoring of matches and mismatchesĪ better approach for global pairwise alignment using the Needleman-Wunsch algorithmĪutomating Needleman-Wunsch alignment with PythonĪutomating Smith-Waterman alignment with Python Step 4: Transcribe some of the possible alignments that arise from this process. Step 2: Add values to the cells in the matrix. Step 1: Create a blank matrix where the rows and columns represent the positions in the sequences. A first algorithm for aligning a pair of sequences
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