Web Reference: In this section you will optimally align two short protein sequences using pen and paper, then search for homologous proteins by using a computer program to align several, much longer, sequences. May 27, 2025 · We’re going to take a look at just the basics of sequence alignment to get you started. How many sequences can I align? You must have a minimum of 2 sequences to perform an alignment. For comparing 2 sequences you’ll need to perform a “pairwise” alignment. When performing sequence alignments it is important to realize some of the key differences between aligning nucleic acid sequences and aligning protein sequences.
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