DCA - Manual

Sequence Format:
DCA supports sequences in FASTA format via file upload or copy&paste in a textfield. A sequence in FASTA format begins with a single-line description, followed by lines of sequence data.

• The description line starts with a greater than symbol (">").
• The word following the greater than symbol (">") immediately is the "ID" (name) of the sequence, the rest of the line is the description.
• The "ID" and the description are optional.
• all lines of text should be shorter than 80 (normally 60) characters.
• the sequence ends if there is another greater than symbol (">") symbol at the beginning of a line and another sequence begins.

    >sequence_1
    GLAKDAWEIPRESLRLEAKLGQGCFGEVWMGTWNDTTRVAIKTLKPGTMSPEAFLQEAQVMKKLRHEKLVQLYAV
    VSEEPIYIVIEYMSKGSLLDFLKGEMGKYLRLPQLVDMAAQIASGMAYVERMNYVHRDLRAANILVGENLVCKVA
    DFGLARLIEDNEYTARQGAKFPIKWTAPEAALYGRFTIKSDVWSFGILLTELTTKGRVPYPGMVNREVLDQVERG
    YRMPCPPECPESLHDLMCQCWRKDPEERPTFKYLQAQLLPACVLEVAE

Substitution Matrix:
DCA provides following substituion matrices: PAM250, PAM160, Blosum30, Blosum45, Blosum62, DNA/RNA, and unit cost.

Free shift:
DCA by default does not penalize gaps at either end of the sequences to make the compensation of differences in the length of the seuences free of charge. This free shift option can be deactivated.

Approximate Cut Positions:
The last, most time consuming phase of the search for cut positions can be deactivated so that the sequences are cut at approximate slicing positions, which generally yields slightly less accurate but often much faster alignments. A more decent explanation of this heuristic is found here.

Recursion stop size:
The recursion stop size can be set to any number L ≥ 1. Of course, too large an L (e.g. L > 100) can result in very long running times and very big memory usage due to the resulting MSA-runs. On the other hand, too small an L (e.g. L < 5) can result in empty subsequences at the end of the iteration which may lead to bad alignments.

Window size:
To correct the alignment in the proximity of division sites, the sequences can be re-aligned inside a window of size W ≥ 0

Weight intensity:
The weight intensity λ can be set to any value between 0 (no weighting) and 1.0 (max. weighting). Here is the formula.