Work

Extending Biopython to combine multiple sequence alignments with the same reference into a Multiple Sequence Alignment.

Year: 2025

Type: article

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.

Source: PubMed

DOI: 10.17912/micropub.biology.001966

Authors: Cassia Bastress, Michiel de Hoon, Manuel Lera-Ramirez, Jürg Bähler

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funders: UK Research and Innovation, Ministry of Education, Culture, Sports, Science and Technology, Engineering and Physical Sciences Research Council, RIKEN

Award: Genestorian: a web application to document and trace genetic modifications in model organism and cell line collections.

OpenAlex ID: W7130368680