Sequencing Modes - There are two modes for sequence data analysis.

In 'guide/reference' mode, sequencing data is aligned and compared to a 'wildtype' DNA sequence. Guide/Reference mode is useful when you know what sequence you are expecting. For example, you might be sequencing PCR products to be used in a subcloning experiment, and you want to confirm that no mutations (or expected mutations) have been introduced during the PCR reactions. In this mode, the 'guide/reference' sequence is shown at the top of the alignments, together with a translation and annotations if required.

In 'consensus' mode, sequences are assembled into a contig to form a new 'consensus' sequence. Consensus mode is used when the sequence being analysed is unknown, eg in library screening.

How to set the Guide/Reference Sequence

Open a DNADynamo window that contains the DNA sequence that you want to use as the 'guide/reference' sequence, then select menu options 'Sequencing' -> 'Open and Align Sequence Data Files To This Windows Sequence (.abi/.scf/.fasta/.txt/.cow)'

How to assemble a new contig/consensus

select menu options 'Sequencing' -> 'Open and Assemble Sequence Data Files To Form A New CONTIG (.abi/.scf/.fasta/.txt/.cow)'

Alternatives - you can also access consensus vs guide/reference mode via the file 'MANAGER' and the 'Alignments' button