This three-part tutorial illustrates the utility of pairwise alignments when comparing mRNA transcripts to their cognate genes. This example begins with multiple alignments of the alcohol dehydrogenase (ADH) gene from Drosophila melanogaster and four mRNA transcript isoforms. Comparing the overview of the alignment to the gene’s annotations reveals a few problems that are easily resolved with pairwise alignments.
As in Try It! – Follow a multiple alignment with Global pairwise alignments, a global alignment is the most suitable approach, because long gaps corresponding to introns may make it hard for a local aligner to join segments from exons. With a local alignment the ends of a transcript may not be included among the aligned segments.
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