When you load two or more DNA or protein sequences into sequence channels, the Sequence | Alignment | Two Sequence Alignment menu is activated. You may accurately compare two sequences with this function. Another advantage of using this function is that you may quickly align any region of the two DNA or protein sequences by defining analysis regions (see the section VI.2).
A dialog box appears by selecting the Sequence | Alignment | Two Sequence Alignment command. You should specify the following parameters.
1)K-tuple indicates the minimum number of identical bases in an exactly matching fragment. The K-tuple value is from 2 to 7 for DNA and from 1 to 3 for protein. The default level is 4 for DNA and 2 for protein. Increasing the K-tuple may decrease the sensitivity for alignment and slightly speed up the alignment.
2)Gap penalty defines the penalty score for each gap insertion. A score of +1 is given to one matched base between the two sequences and a negative score for a gap insertion. A gap penalty is from 1 to 99. The default level is 7.
1)Gap open penalty is a negative score for opening each gap.
2)Gap extension penalty is a negative score for extending each residue in an existing gap.
Click the OK button to perform alignment and display the alignment results in a text window. DNAMAN includes the percentage of homology in the result window.
The identity (%) of the two sequences is calculated using the following formula:
Number of identical bases or AAs between two sequences
Identity (%) = 覧覧覧覧覧覧覧覧覧覧覧覧 ×100
Length of aligned sequence - Length of all gaps
DNAMAN shows also the gaps introduced in the alignment.
Number of gaps of both sequences
Gap (%) = 覧覧覧覧覧覧覧覧 × 100
Length of aligned sequence