In addition to the 200 + EMBOSS and EMBASSY programs that can be used through the Jemboss interface, there are three utilities that offer a graphical analysis of certain results.
A multiple sequence viewer written and supported by the EMBOSS team, this is also available as a standalone utility from http://emboss.open-bio.org/Jemboss/ as well as being a tool attached to the Jemboss interface. It reads any sequence in FASTA or MSF format.
Any number of JAE windows may be opened at any one time.
str into the Jemboss
GoTo box to select the
stretcher application. Enter
uni:bgal_ecoli into the first
Sequence Filename field and
uni:bgal1_entcl into the second.
LOAD SEQEUNCE ATTRIBUTES for both sequences. Alter the
align format drop down menu to read
fasta (scroll up) and hit
GO. Save the results to a local file (Section 22.214.171.124, “Saving Analysis Results”) as
bgal_align.fasta and closed the Saved Results window.
If using the standalone version downloaded from the above mentioned OpenBio page: Select the
File menu and the
Open option and navigate to the
bgal_align.fasta file. Open the file.
Open option does not default to the specified local home directory location (Section 9.7.1, “Directory location”) and must be navigated to.
If using the viewer attached to the Jemboss interface: Open the local file manager (Section 9.3.1, “Local File Management”) and navigate to the
bgal_align.fasta file. Highlight this file and right click to reveal the file management menu (Section 9.3.6, “File Manipulation”). Select
Open with and then the
Jemboss Alignment Editor option.
From the main Jemboss window, it is also possible to use the
Tools menu and select the
Multiple Sequence Editor ; Jemboss utility. Use the
File/Open menus to retrieve the alignment file.
The alignment can be manipulated by dragging residues or nucleotides to the right or left to create or close gaps.
Highlight both sequences by clicking on each in turn and hit the
Lock button at the bottom left of the viewer.
If a sequence is highlighted in error then a further mouse click will un-highlight it.
Mouse over the fifteenth position of the E. coli sequence and drag the arginine residue to the right. The other sequence also moves at the same point.
To unlock the sequences hit the same button (it now says
Edit/Unlock All Sequences options can also be used instead.
The sequence text size can be altered using the drop down menu to the right of the
Calculate menu on the toolbar.
This can be accessed by selecting a residue and clicking with the right hand mouse button. In addition to the menu options, the sequence containing the selected residue is reported.
delete option removes the entire sequence from the display. Currently this operation cannot be undone without reloading the entire alignment back into the JAE.
This is for nucleotide sequences only. Further options to reverse and/or complement the sequence separately are available from the menu.
Sequences can be trimmed at both the 5' and 3' ends to accommodate alignments between sequences with loosely configured termini.
Edit menu and the
Trim Sequences option. Alter the start to
15 and the end to
1016 to remove the sequence termini. Hit the
There is currently no way to reinstate the trimmed termini without re-loading the whole alignment.
Insert Annotation Sequence option is accessed from the
Edit menu and allows a sequence to be annotated with further data which can be
Read from File or entered via Cut and Paste into the entry box. Any sequences must be pasted using the
<CONTROL>+V shortcut. Accepted formats are
Options in the
View menu offer various options to display the alignment data. Options are available to colour the text or the white area surrounding the text as the
colour boxes options respectively.
View menu at the top of the Editor and then the
Find Pattern option. Enter
LILC into the field and hit the
Find button to reveal the area immediately before the active site glutamate. Close the Find Pattern window.
The last pattern to be searched will remain in the entry field until either a new pattern is selected or the JAE session is halted.
Find patterns is not case sensitive. The wrap around option is selected by default and ensures the pattern is searched for within the whole sequence and not simply the portion of sequences following the cursor. The same pattern may be used to search in multiple places in the sequence.
Displays all protein and nucleotide alignment matrices.
View menu and
Matrix Display option to reveal the default Blosum62 scoring matrix grid. Highlight the
EPAM250 matrix from the right hand pane and hit the
Set button. The new matrix will be reported in the main JAE window.
The new scoring matrix will then apply to calculations of the consensus sequence (Section 126.96.36.199, “Consensus Sequence”). The current matrix is reported at the bottom left of the alignment viewer. The set matrix display will be remembered for the duration of the JAE session.
Close the matrix display box.
Specifies the colour for a given amino acid.
Colour Display option from the
View menu. Right click on the colour box against the arginine (R) amino acid and select the
colour option that appears. Select light blue (R128, G192, B255 on the tooltip) and confirm selection with a left mouse click.
The changes are effected in the alignment viewer.
Close the Colour window.
Alters the display to colour amino acids according to selected properties. The default selection is
Residue Colour and the white area surrounding the text is coloured with the appropriate hue. This can be turned off by deselecting the
colour boxes option at the bottom of the
View menu but coloured boxes reappear when a different scheme is selected. The selected colour scheme is reported at the bottom of the alignment display.
Colour by Property option indicates which property is represented by which colour. This selection may be useful for identifying regions of functional or structural similarity.
View menu and
The colour selection for each match can be altered by left clicking on the default colour and selecting a new one from the available palette. The default box selection can be altered to change the display image of the alignment.
Identity Number (Section 188.8.131.52, “Identity Number”) as
2. Alter the
Threshold for positive matches (Section 184.108.40.206, “Threshold for Positive Matches”) to
Identity Colour represents the actual text and the
Background Colour represents the area around the text.
Set button to effect the changes in the Viewer. Close the
Colour Matches box.
Box option to remove the black line drawing around areas of identity and similarity.
This selects which matches are coloured as identical and that selection is based on how many of the amino acid residues in a specific position are identical. The default is always the number of sequences in the alignment.
Identity Table option from the
Calculate menu to see that the current alignment affords a 64% identity between the two residues. Move several residues to the right (Section 220.127.116.11, “Sequence Manipulation”) and re-select the
Identity Table option. Note the difference in the identity.
Any score greater than zero according to values in the selected scoring matrix.
Options in the
Calculate menu are designed to offer an alternative calculation of the information contained in the alignment display.
emma from the
Alignment/MULTIPLE menus (Section 9.4.2, “Program Categories”) in the main Jemboss window and then in the
sequence filename field in the
input section type
uni:bgl*_arath and hit
GO. Retrieve the results from the Job Manager (Section 9.6.3, “Job Manager”) and save the
bgl10_arath.aln file to the local file manager (Section 18.104.22.168, “Saving Analysis Results”) as
File menu on the Jemboss Alignment Editor and open the new alignment file.
Calculate menu and select the
Calculate Consensus option.
Once the initial calculation has been done, the menu option subsequently reads
Scroll to residue 64 to see the start of the consensus sequence
This calculation is based on the EMBOSS program
cons. It may be affected by altering the scoring matrix (Section 22.214.171.124, “Matrix Display”) and the Consensus Options (see below) and thus should be recalculated after every change to these parameters. The consensus sequence may be removed from the display at any time using the delete option on the
Sequence Manipulation Menu (Section 126.96.36.199, “Sequence Manipulation Menu”).
Set consensus options from the
Calculate menu to show the
Consensus Options box.
The consensus sequence needn't be displayed before these options are set as the display will then appear on screen.
Minimum positive match score value for there to be a consensus option to
6. The residue
G disappears from this consensus run with a plurality value of 6.
Minimum positive match score represents the plurality value. A consensus sequence will be displayed if the resulting score*weight calculation of the sequence equals or exceeds this value. The default is 0.5 per sequence in the alignment which is equal to half a default weight for each sequence of 1. Values to several decimal places will be accepted in this field.
Alter the plurality value back to
4.5 and alter the
Minimum number of identities for there to be a consensus to
6. Hit the
Calculate Consensus button. The
S residues disappear from the sequence as there are only 5 and 4 of them in positions 64 and 69 respectively.
Only whole numbers may be entered into this field. This parameter is based on the number of identities in a specific position, but both this and the plurality value requirements must be fulfilled before a consensus is shown.
6 in the
plurality value field. The consensus run now appears as
Increase the value of the
Threshold positive match score for setting the consensus to uppercase to
6 and hit the
Calculate Consensus button. The remaining consensus run is now displayed in lower case characters. Alter the value to
5 to reinstate upper case letters.
Residues in the consensus will be set in uppercase only if their plurality value exceeds the
Threshold positive match score. Values to several decimal places will be accepted in this field.
Any alterations in the
Consensus Options box will be deleted once the window is closed, although the altered consensus sequence will remain in the display until it is removed or the alignment window is closed.
The consensus sequence may be saved using the
File/Save Consensus options. The consensus sequence must be visible on the display before it can be saved.
Calculate menu and select the
Calculate Consensus plot option. The plot will appear underneath the alignment.
This plot is based on the calculations used in the EMBOSS program plotcon which plots the graph based on the percentage identity of each sequence in the alignment.
Once calculated the menu option reads
Recalculate Consensus Plot and this must be selected if the matrix used for the alignment is altered. Calculated consensus plots can be removed from the display by right clicking the consensus sequence and then selecting the
Accessed from the
Calculate menu. Calculates pairwise percentage identity between each sequence in the alignment. This calculation is a simple percentage score of identical matches within the multiple alignment as displayed.
This option rearranges the alignment display to list the sequences in the alignment in alphabetical order.
File menu and
Save As option to save the manipulated alignment to a local file. The
Save Consensus option stores the consensus sequence only to a local file.
The alignment may be printed to paper or as a graphic.
File menu and the
Print Preview option. Select single page and alter the
Residues per line to
25 and view the results. Return to
File menu and select
Print Image Files from the submenu. Hit
OK on the
Page Setup box and in the subsequent
Save box, alter the
Residues per line on the right hand side to
25 and select
JPG from the drop down menu. Alter the file name to
Save to an appropriate location. Five images have now been saved.
Should the graphic need to appear on paper, it will be printed on five sheets. Select the
Print Postscript option and alter the page setup and number of residues per line as requested in the two subsequent boxes. Alter any printer properties before printing. There may be slight delay between the
Page Setup box disappearing and the
Options box appearing.
Page Setup and
Options boxes appear when the
Print Preview for
Multiple Pages is selected. Anything in these boxes may be altered and previewed before committing the graphic to paper.
The single image may be printed or previewed. In this case, the only option offered is the number of
Residues per line.
This is a basic drawing package that offers a graphical representation of the features within a nucleotide sequence. It is accessible from the
Tools menu on the Jemboss main window. This utility is also available as a standalone option from http://emboss.open-bio.org/Jemboss/. Jemboss itself does not need to be downloaded in order for this to function.
If this editor is opened in error then a graphical display will result when the editor is closed again. This display should simply be closed (and thereby deleted) if it is not required.
Use the mouse or the
TAB key to move around to various entry fields as use of the return key will create the graphic before all the features have been added.
Access the DNA Editor from the Jemboss
Access http://emboss.open-bio.org/Jemboss/ and hit the red
JEMBOSS DNA EDITOR button.
Accept the security filter (if launching from the website) and hit
OK on the Jemboss DNA Viewer wizard to create a new DNA display. In the
DNA Attributes section, alter the type of graphic to
linear and enter
7477 in the
stop entry field. Alter the
Tick Interval on the right hand side to
1000 and the
Minor Tick Interval to
Genetic Feature section, enter
79 in the
1161 in the
stop fields (overwriting the previous numbers) and hit the
Add Feature button. Double click on
CDS in the
Label column of the
Genetic Feature table and alter the text to
LacI. Hit return to confirm text entry.
4358 in the
stop fields. Hit the red square and alter the colour to green, confirming with the
OK button on the colour palette. Hit the
Add feature button and alter the
Label text in the
Genetic Feature table to
lacZ and confirm by hitting return. Alter the
line width to
7 using the slide bar.
Should a feature have been added in error then there is currently no way of deleting it from the table using the editor wizard, but it must be deleted after the graphic has been created.
Line width may also be entered directly into the field to the right of the colour square.
Restriction Enzymes section, enter
159 in the
Position fields respectively. Hit the
Add RE button.
OK button at the bottom of the wizard to produce the graphical output.
The Editor can read files created by the programs
cirdna and write them out to the DNA Viewer (Section 188.8.131.52, “DNA Viewer”). This option is available as an alternative to the
create a new DNA display (Section 184.108.40.206.1, “Create New DNA Display”) option on opening the DNA Editor.
This option is only available from the DNA viewer (Section 220.127.116.11, “DNA Viewer”) and allows a return to the DNA Wizard in order to alter the original data.
Contains the graphical output created by the DNA Editor and offers all options included in the wizard and some additional features to edit the graphic. The graphic can be viewed as a larger or smaller image using the
View menu and
Zoom In and
Once this Viewer is closed, the data is lost unless it has been saved (Section 18.104.22.168, “Print”) or if the original data was available as a
cirdna file (Section 22.214.171.124.2, “Read in Data File”)
Used as above, and accessed from the
options menu. Options to create a new file (Section 126.96.36.199.1, “Create New DNA Display”), read in a datafile (Section 188.8.131.52.2, “Read in Data File”) and edit currently displayed data (Section 184.108.40.206.3, “Edit Data File”) are available.
Contains all DNA attributes found in the DNA Editor. To alter a feature in the graphical output, enter the relevant value in any of the fields and hit the
return button to effect the change in the graphic.
Contains the same tick mark information as the DNA editor. Alter the text and press the
Set button to effect the change in the graphic.
Contains the same Genetic features information as the DNA editor. Text may be altered in the table by double clicking on the relevant entry field, altering the text and hitting return to confirm input. The colour of a feature may, as for the DNA editor, be altered within the table. Select the current colour and alter it using anyone of the three colour palette tabs offered.
Should a feature have been mistakenly added, highlight it and delete using the
Tools/Delete Selected Row option. This delete option is only available in the DNA Viewer.
Contains the same restriction enzyme information as the DNA editor. New restriction positions can be added or existing positions can be deleted.
There are options under the
File menu to print the final graphic to paper (
Print Postscript option) or to an image file. If the
Print Postscript option is chosen then the data will be sent by the print wizard to the printer you will select. An actual postscript file may be saved by selecting the
Print to File option on the print wizard (if you have any postscript printer installed and you have selected it).
Once the graphic is complete, hit the
File menu and select the
Print png/jpeg image option. Click
OK in the
Page Setup box. Select an appropriate folder and rename the image in the
Save box. Hit the
The saved image can be used in subsequent documents.
Close the DNA Viewer.
This is third party software, written originally by Michele Clamp. All downloads and documentation are available from http://www.jalview.org/. This multiple sequence viewer can be accessed in Jemboss via the
Tools menu on the main Jemboss toolbar. Any errors found within this software cannot be fixed by the EMBOSS team, although they will pass any reports on to the relevant people.