ArticlemicroPublication biology2026
Extending Biopython to combine multiple sequence alignments with the same reference into a Multiple Sequence Alignment.
Article in microPublication biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Pairwise alignments (PWAs) are commonly used to compare sequences to a reference. Existing alignment tools provide algorithms to align multiple sequences to a single reference and to merge two sets of aligned sequences; but not to combine individually aligned PWAs with a common reference into a single MSA which preserves their original alignment structure. This is required for certain workflows. One example is aligning multiple sequencing traces with a circular plasmid sequence for validation. Some alignment tools that take into account the circularity of the plasmid sequence return a PWA per sequencing trace. For visualization, all PWAs have to be combined into a single MSA. For this purpose, we developed an algorithm that combines alignments sharing the same reference into an MSA, and implemented it as a classmethod in Biopython's Alignment class.
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