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