View alignments
The basic options for viewing alignments are the same as for viewing sequences, described in View sequences.
Alignment specific view options in the Sequence layout, Nucleotide info, Alignment info, and Positional stats side panel tabs, to the right of the view, are described here.
Sequence layout
In the side panel tab Sequence layout the option Alignments on top supports moving the aligned sequences relative to other elements shown in the alignment view. When checked, the alignment is shown at the top of the view, when unchecked the alignment is shown underneath other included summary information such as Consensus, Conservation and Sequence logo.
Nucleotide info
In the side panel tab Nucleotide info under Translation, there is an extra checkbox: Relative to top sequence. Checking this box will make the reading frames for the translation align with the top sequence so that you can compare the effect of nucleotide differences on the protein level.
Alignment info
The entire side panel tab Alignment info is specific to alignments. Each of the options in the Alignment info relate to each column in the alignment.
The data points for graph representations can be exported (see Export graph data points to a file).
Consensus
Shows a consensus sequence at the bottom of the alignment. The consensus sequence is based on every single position in the alignment and reflects an artificial sequence which resembles the sequence information of the alignment, but only as one single sequence. If all sequences of the alignment is 100% identical the consensus sequence will be identical to all sequences found in the alignment. If the sequences of the alignment differ the consensus sequence will reflect the most common sequences in the alignment. Parameters for adjusting the consensus sequences are described below.
- Limit This option determines how conserved the sequences must be in order to agree on a consensus. Here you can also choose IUPAC which will display the ambiguity code when there are differences between the sequences. For example, an alignment with A and a G at the same position will display an R in the consensus line if the IUPAC option is selected. The IUPAC codes can be found in the Appendix. Please note that the IUPAC codes are only available for nucleotide alignments.
- No gaps Checking this option will not show gaps in the consensus.
- Ambiguous symbol Select how ambiguities should be displayed in the consensus line (as N, ?, *, . or -). This option has no effect if IUPAC is selected in the Limit list above.
The Consensus Sequence can be opened in a new view, simply by right-clicking the Consensus Sequence and click Open Consensus in New View.
Conservation
Displays the level of conservation at each position in the alignment. The conservation shows the conservation of all sequence positions. The height of the bar, or the gradient of the color reflect how conserved that particular position is in the alignment. If one position is 100% conserved the bar will be shown in full height, and it is colored in the color specified at the right side of the gradient slider.
- Foreground color Colors the letters using a gradient, where the right side color is used for highly conserved positions and the left side color is used for positions that are less conserved.
- Background color. Sets a background color of the residues using a gradient in the same way as described above.
- Graph Displays the conservation level as a graph at the bottom of the alignment.
The bar (default view) show the conservation of all sequence positions. The height of the graph reflects how conserved that particular position
is in the alignment. If one position is 100% conserved the graph will be shown in full height.
- Height Specifies the height of the graph.
- Type The type of the graph: Line plot, Bar plot, or Colors, in which case the graph is seen as a color bar using a gradient like the foreground and background colors.
- Color box Specifies the color of the graph for line and bar plots, and specifies a gradient for colors.
Gap fraction
Which fraction of the sequences in the alignment that have gaps. The gap fraction is only relevant if there are gaps in the alignment.
- Foreground color Colors the letter using a gradient, where the left side color is used if there are relatively few gaps, and the right side color is used if there are relatively many gaps.
- Background color Sets a background color of the residues using a gradient in the same way as described above.
- Graph Displays the gap fraction as a graph at the bottom of the alignment.
- Height Specifies the height of the graph.
- Type The type of the graph: Line plot, Bar plot, or Colors, in which case the graph is seen as a color bar using a gradient like the foreground and background colors.
- Color box Specifies the color of the graph for line and bar plots, and specifies a gradient for colors.
Color different residues
Indicates differences in aligned residues.
- Foreground color Colors the letter.
- Background color. Sets a background color of the residues.
Sequence logo
A sequence logo displays the frequencies of residues at each position in an alignment. This is presented as the relative heights of letters, along with the degree of sequence conservation as the total height of a stack of letters, measured in bits of information. The vertical scale is in bits, with a maximum of 2 bits for nucleotides and approximately 4.32 bits for amino acid residues. See Bioinformatics explained: Sequence logo for more details.
- Foreground color Color the residues using a gradient according to the information content of the alignment column. Low values indicate columns with high variability whereas high values indicate columns with similar residues.
- Background color Sets a background color of the residues using a gradient in the same way as described above.
- Logo Displays sequence logo at the bottom of the alignment.
- Height Specifies the height of the sequence logo graph.
- Color The sequence logo can be displayed in black or Rasmol colors. For protein alignments, a polarity color scheme is also available, where hydrophobic residues are shown in black color, hydrophilic residues as green, acidic residues as red and basic residues as blue.
Positional stats
The side panel tab Positional stats provides site specific information about the alignment. Hover the mouse cursor over a position in the alignment or make a selection to populate the tab with information (figure 16.8).
Figure 16.10: Contents of the Positional stats tab when a single sequence is selected (Left) and when three sequences are selected (Right). Note that the side panel can be dragged into the alignment view.
When one position is selected, the information provided is calculated from all the sequences at the position. If more sequences at the same position are selected, the information is calculated for the selected sequences only.
The following information is provided:
- Alignment position The selected position in the alignment.
- Pairwise % identity Average percent identity. All pairs of bases at the same position are compared. The number of identical pairs is counted and divided by the total number of pairs. The count of ambiguity characters is scaled to the number of bases they can represent, for example a G compared to an R (A or G) is given the value 0.5.
Example calculation for an alignment with the nucleotides A, A and G in the tested position: There are three pairwise comparisons, A to A = 1, A to G = 0, and A to G = 0. The pairwise % identity is then 1/3.
- A, C, G, T and - Percentage of A, C, G, T and "no nucleotide" at the selected position.
Subsections