Plasmid alignments

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You can seamlessly align whole plasmid sequencing reads in Benchling using circular DNA sequences as templates. Benchling automatically rotates the sequences in the alignment when needed, and the alignment’s chosen index position doesn’t change the index stored on the sequence itself.

Whole plasmid sequencing

When the input sequences are all approximately the same length as the template (+/- 10% in length), the alignment tool pre-processes all inputs by treating them as circular and optimally rotating them using the MARS tool.

When the rotation is successful, the template remains linearized at the same position and all other rows are rotated to match, if necessary.

Note: Reads are treated as circular, even if they are imported in a file format or are an existing Benchling sequence that is not explicitly circular. For example, if aligning a circular template against a FASTA file where all reads are a similar length to the template, the tool rotates them as plasmids even though FASTA format does not encode circularity.

Cross-origin short reads

If the input sequences are 10% longer than the template, then the template sequence is doubled before aligning and rotated so no reads cross the origin. For example, aligning across the midway point in the doubled template.

If there is complete coverage of the template, the template alignment will remain linearized and split any cross-origin rows so the middle portion is all gaps.

What if my alignment fails?

If the alignment process fails, manually re-index of the template plasmid, then try again.

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