Multiple sequence alignment methods

Algorithms

DNAMAN uses ClustalW algorithm (Feng-Doolittle and Thompson) for Optimal Alignment, and the global alignment algorithm (Wilbur and Lipman) for fast alignment. The three types of Optimal Alignment in DNAMAN provide high quality alignment results. With the Fast Alignment method, you may quickly align a large number of DNA or protein sequences.

Parameters and Methods

You may set different parameters to make adequate alignment for your DNA or protein sequences.

There are four types of alignment:

• Full alignment to completely align all sequences.
• Profile alignment to align two multiple alignment profiles without disturbing the original alignments.
• New sequence on profile to align a new sequence with an existing multiple alignment profile.
• Fast alignment.

Multiple sequence alignment editor

DNAMAN provides a high performance alignment editor. A graphical view of the alignment allows you to quickly move to an interesting region. You can change the alignment list order by drag and drop sequence names. You are also able to add or delete gap insertions, move a fragment within a gap and truncate aligned sequences.

You can modify the appearance of multiple alignment sequences:

• displaying identical residues in colors or blocks
• displaying consensus sequence
• changing text font

Multiple alignment input and output

You can directly input sequences or multiple alignment profiles for alignment from the following sources:

• GenBank,
• EMBL/Swiss Prot,
• GCG/MSF,
• CLUSTAL,
• FASTA,
• NBRF/PIR
• GDE

The multiple alignment editor can output an alignment in different formats: GCG/MSF, CLUSTAL, NBRF/PIR, and GDE. The multiple input and out put capacity of DNAMAN makes it compatible with major sequence analysis software.

Phylogenetic trees

DNAMAN calculates the homology matrix and establishes related distances between all pairs of sequences. Consequently, DNAMAN can output a distance matrix of multiple alignment, and draw phylogenetic trees or homology trees. You can carry out bootstrapping tests for the confidence value of a phylogenetic tree.

Restriction analysis

If the sequences in multiple alignment editor are DNA, you can perform a restriction analysis on these sequences. This analysis is useful in restriction site comparison of aligned DNA sequences.

Hydrophobic / hydrophilic profiles

If the sequences in multiple alignment editor are protein, you can plot the hydrophobic or hydrophilic profile of all sequences for comparison.

Protein secondary structure prediction

DNAMAN predicts the secondary structure of multiple protein sequences using the DSC method developed by King and Sternberg.