The Multiple Alignment Sequence Editor of DNAMAN (MASED) is an efficient tool for multiple sequence editing. You may use MASED to visualize multiple alignments and analyze sequence homology. The results of the Multiple Alignment function are loaded directly into MASED. You may also use MASED to analyze the multiple alignments produced by other programs such as GCG. MASED recognizes all multiple sequence formats listed in the pages 7-12. When you use the File | Open special | Multiple alignment command to open these files, DNAMAN loads them into MASED.
Press the Options button in MASED to open the property pages.
In the Preferences page you may change the following properties of MASED:
By default, all sequences in MASED are shown. However, you can select some of them to display. Any sequence deselected in the display box will be hidden in the MASED window. You may press the All button to select all sequences in the list.
You can specify the sequence as DNA, Protein, or as detected by DNAMAN. The Auto detect option will assume the sequences as DNA or protein according to their compositions. This method makes correct assumptions in 98% cases. If your sequences have extreme compositions, you should specify them as DNA or protein sequences.
If you specify the sequences as DNA, you may display translated amino acid sequences in MASED. By choosing one the three reading frames, you may display the amino acid sequences in the editor.
When you print out, copy or export alignment as DNAMAN text file, the text length of each line has to be defined. You should choose a line length according to the paper size and text font. The default length is 40.
You may select any font for MASED. However, it is highly recommended to use fixed size fonts. Only fixed size fonts make the sequences correctly aligned.
Check this option if you like to have all sequence shown with the same length. DNAMAN fills shorter sequences with dots. If this option is not checked, DNAMAN will stop at the last letter of a sequence and leave empty space thereafter.
MASED will display consensus sequence of the alignment if you check the Show Consensus Sequence option. Consensus residues can be defined as Identical bases or amino acids at each position, or as Homology residues at each position. If you choose Homology residues, the cutoff level for homology residues must be defined in the Shading Homology page.
If you have selected this option, a graphic presentation is shown on the top of the sequence position labels. The graphic pattern represents the homology level along the sequence profile. Strong signal means high homology level. A red rectangle box on the graphics indicates the sequence region currently displayed on the MASED window. By clicking on the graphic overview, you can move the displayed window to any region of the sequence profile. The overall percentage of the sequence identity is shown on top of the graphic presentation. This percentage is calculated according to the homology level of each position of all the sequence.
This option defines how to edit a sequence. If this option is checked when you want to insert or remove gaps in the middle of a sequence, DNAMAN will make changes at downstream to make next sequence block unchanged. Therefore, insertion or removal of gaps will have little compact for downstream sequence. If this option is not checked, insertion or removal of gaps will modify entire downstream sequence.
In the Shading Homology page you may modify the following parameters:
DNAMAN may shade a position to show the homology. There are five options available: Non, 100%, >=75%, >=50% and >=33%. If you choose the >=50% option, all positions with 50% or higher homology will be highlighted. For example, if there are 10 sequences in the multiple alignment and 5 or more sequences show the letter "A" in position 2, position 2 will be highlighted.
You may highlight homology regions with Colors, or Blocks, or both. If the Colors option is checked, you may define any color for different levels of homology. If the Blocks option is checked, you may define the thickness of lines to highlight the blocks.
This option applies only to protein sequences. If this option is checked, DNAMAN will shade similar amino acids. The similar amino acid is defined in the “similaa.dat” file in the DNAMAN system folder
There are many functions of MASED for sequence analysis and edting:
- Shading homology regions
- Changing list order
- Moving a sequence fragment between gaps
- Truncating aligned sequence fragments
- Adding and deleting gap insertions
- Exporting multiple sequences in different formats
- Copying
- Producing trees
- Performing restriction analysis of DNA sequences
- Predicting secondary structures of protein sequences
- Comparison hydrophobic/hydrophilic properties of protein sequences
In a multiple alignment profile, homology regions are easier to visualize when they are highlighted. In MASED, these regions can be highlighted according to their homology level. Depending on your preference, either line blocks or colors can be used to shade the homology regions.
Press the Options button in MASED to open the property pages. See the previous section for the information of Shading homology.
If you choose the File | Print Preview command, DNAMAN displays the aligned multiple sequences with the shading colors in a printing view window.
All sequence names are listed in the left panel of MASED. To change the output sequence order:
You may want to move a sequence fragment that is misplaced between gaps.
1) Select the sequence you want to move. For example, selecting CTGAA:
CAC..CTGAA............TTACTGCCAAGGATATCCTCGAC
2) Upon selecting, the cursor switches to an arrow. Move the arrow to a location where you want to insert the fragment. Now, click the left mouse button to place the fragment there.
CAC..............CTGAATTACTGCCAAGGATATCCTCGAC
You may move the fragment only between the gaps that do not affect sequence position.
If you are interested in only a small region of the multiple alignment, you may delete flanking regions of the alignment. In other words, you may delete both ends of the alignment.
1) Place the cursor in the beginning or at the end of the first sequence of the alignment.
2) Use the Shift+Arrow keys or the mouse to select the fragments.
You can truncate a part of one sequence by selecting the sequence from its beginning or the end and using the Delete or the Backspace Key to delete the selected sequence.
You cannot delete any nucleotide or amino acid located in the middle of the alignment.
A dot represents a gap insertion in the multiple alignment. DNAMAN allows adding or deleting one or more dots in the alignment. When you add or delete gaps, the downstream alignment may or may not be altered by this change. See the Synchronize gaps option in the Properties of MASED.
1 10 20 30 40 50
Seq1 TTTGACTGCCACTTCCTCGAAGAAGGTTTACTGCCAAGGACATTCTGGAC //
Seq2 CAC........CTGAA...........TTACTGCCAAGGATATCCTCGAC //
Adding 5 dots between CT and GAA of Seq2:
1 10 20 30 40 50
Seq1 TTTGACTGCCACTTCCTCGAAGAAGGTTTACTGCCAAGGACATTCTGGAC //
Seq2 CAC........CT.....GAA......TTACTGCCAAGGATATCCTCGAC //
When you click the Output button in MASED, a popup menu appears. Choose the Sequence File menu to export the alignment into a text window using one of the seven formats. The sequence in the text file is not marked with shading colors to indicate the identical residues.
If there are only two sequences in MASED, choose the Two Sequence Alignment command. If the sequences are DNA you can display the identical bases in *, | or : . If the sequences are protein, DNAMAN will indicate the identical residues as well as the similar amino acids.
Example:
Alignment of 1(upper line) and 2(lower line)
Identity=14% Similar residues=56%
-----------------
1 RFSEVSSVFTTRLHTLNGLFSLCALTRFIRENRISHLMIHTGKIAALSILLKKLTGVRLI
:: :.|.|:. ::.:. | .|. |:: | ..: .:.:.: .: :| . .:|
1 HYIGFSKVYKRLFQKWTRLDPLPYSQRIL..NIRDKVTTQEDSVIVIHNSMKLYRQIRER
61 FVKHNVVANKTDFYHRLIQKNTDRFICVSRLVYDVQTADNPFKEKYRIIHNGIDTDRFP.
.. .:| :. : :.. :..|..::|..|.:: .. .. | . |:.||: .: :.
59 NPNAKLVMHMHNAFEPELPDNDAKIIVPSQFLKAFYEERLPAAAVS.IVPNGFCAETYKR
In many cases such as preparing posters or slides, you may want to generate a document in which some residues in multiple sequence alignment are identified. DNAMAN allows you to copy a part of multiple sequence alignment from MASED to text window or to other Windows applications.
See the section IX.5
This function can be used to compare the restriction properties of aligned DNA sequences. You can choose any enzymes for restriction analysis. The results are shown in a text window. See the section X.3.1 about the results of Restriction analysis with multiple DNA sequences
DNAMAN uses the DSC method to predict secondary structures of the aligned protein sequences. See the section XI.9 for the description of the function and results.
You can plot the hydrophobic/hydrophilic profiles of the aligned protein sequences. All these sequences are shown in the same plot and indicated in different colors. See the section XI.8 about hydrophobic/hydrophilic plots.
You may save the content of MASED, or export it to a text window. If you choose the File | Save menu, MASED will save the alignment in DNAMAN2 format. The saved multiple alignment profile can be retrieved and edited later.
Output formats of multiple alignment in MASED
Multiple alignment in MASED can be exported to a text window in any of the seven formats:
There are some special options of exporting two sequence alignment (see the previous section).