The right hand side of the status bar is mostly for development purposes
but displays in milliseconds the time taken for the last redraw of the
central sequence panel.
Selected sequences are used in the Colour and Calculate menus.
The Consensus option in the Calculate menu only uses the selected sequences
in its calculation and you can reduce which sequences you display to the
selected ones only by checking the 'Selected only' option in the Colour
menu.
File menu
Input sequences/alignment
Local file
From text box (cut and paste)
URL
Output alignment
To browser
Mail text alignment
Mail postscript alignment
Quit
Font menu
Changes the size of the font for the sequence ids and the alignment.
Smaller font sizes (probably < 6) are of most use if the text is switched
off and the coloured residue boxes only are displayed. The
default font size is 10. This is displayed differently on different
platforms so may not be ideal for your browser.
The only font available is Courier. The reason for this is that a
fixed width font has to be used to speed up the redrawing of the screen.
The alignment sequences are drawn in one chunk rather than one residue
at a time. The font sizes available are :
1
2
4
6
8
10
12
14
16
20
24
View menu
The options in here refer to how each of the residues in the alignment
appears. If the Boxes option is ticked then the residue will appear with
a background colour. (The exact colour depends on which colour
option is selected in the Colour menu.) If the Text option is ticked
then the text is also drawn. If the 'Colour text' option is selected in
the Colour menu then the text colour is set to the colour scheme set in
the colour menu otherwise it is coloured black. Obviously if you
set both the Boxes option and the colour text option you won't see the
residue letters.
If the redrawing speed is too slow for you on your system then turning
off the boxes option will speed it up considerably.
Colour menu
This sets the colour scheme for the residue boxes and the residue text.
Only two colour schemes are available at the moment.
Zappo Colours
The residues are coloured according to their physio-chemical
properties as follows:
| Residues |
Description |
Colour |
| ILVAM |
Aliphatic/hydrophobic residues |
pink |
| FWY |
Aromatic |
orange |
| KRH |
Positive |
red |
| DE |
Negative |
green |
| STNQ |
Hydrophilic |
mid blue |
| PG |
Proline/Glycine (conformationally special) |
magenta |
| C |
Cysteine |
yellow |
PID Colours and 'Bad' Residues
This depends on the applet having performed a consensus calculation on
the alignment. This is done automatically when the applet first starts
up but is not done for subsequent alignment windows. If the consensus
seuqence is calculated again by selecting 'Consensus' from the Calculate
menu then the consensus is calculated for the selected sequences only
and all the alignment sequences are coloured according to that consensus.
This can be useful to display how similar all the other sequences in the
alignment are compared to one (or a few) selected sequences.
The PID option colours the residues (boxes and/or text) according to
the percentage of the residues in each column that agree with the consensus
sequence. Only the residues that agree with the consensus residue
for each column are coloured.
| Percentage agreement |
Colour |
| > 80 % |
Mid blue |
| > 60 % |
Light blue |
| > 40 % |
Light grey |
| <= 40% |
White for boxes/ Black for text |
| 'Bad' residues |
Red |
'Bad' Residues
The PID option also colours residues that are considered 'bad' compared
to the consensus residue. Bad in this context means a negative BLOSUM62
score between the consensus residue and the alignment residue.
Any residues identified like this are coloured red.
Colour Text
Selecting this will change the colour of the residue text characters to
the scheme selected in the Colour menu. Obviously selecting colour
text and boxes means you won't see the text show up.
Selected Only
Only the sequences that are selected in the ID panel are displayed and
coloured.
Calculate menu
Consensus sequence
Each residue in the consensus sequence is the most frequent residue in
each column of the alignment excluding gap residues ' ','-' and '.' .
You can't access the consensus sequence directly but it is used in
the PID colour scheme.
When the editor first starts up the consensus sequence is automatically
calculated using all the sequences in the alignment and the PID colour
scheme is used as default. If the consensus option is selected again
only the currently selected sequences are used to calculate it and all
sequences in the alignment are coloured according to that consensus.
Pairwise alignment (Proteins only)
This calculation is performed on the selected sequences only. Java
is not the fastest language in the world and aligning more than a handful
of sequences will take a fair amount of time.
For each pair of sequences the best global alignment is found using
BLOSUM62 as the scoring matrix. The scores reported are the raw scores.
The sequences are aligned using a dynamic programming technique and using
the following gap penalties :
Gap open : 12
Gap extend : 2
When you select the pairwise alignment option a new window will come
up which will display the alignments in a text format as they are calculated.
Also displayed is information about the alignment such as alignment score,
length and percentage identity between the sequences.
If you want to save that pairwise alignment (it's not in any known format
I'm afraid) you can cut and paste it from the text window with the mouse.
You can also press the 'View in alignment editor' button to bring
up another editor window.
