• Introduction
• File Managers
  • File Manager Manipulation Tutorial
• Launching Applications
  • File Input
  • File Output
  • Input/Output Tutorial
  • Run Parameters
  • Load Sequence Attributes
  • Advanced Options
  • Running the Application
  • Parameter Tutorial
• Results Window
• Saving Results
• Sequence List
  • Add Sequences
  • Remove Sequences
  • Sequence Parameters
  • Sequence List Tutorial
• Jemboss Alignment Editor
  • Editing Alignments
  • Calculating Consensus and Identity
  • Display Options
  • Save Alignment
  • Export Display
  • Alignment Editor Tutorial
• DNA Editor
  • Display Attributes
  • Genetic Markers
  • Restriction Enzymes
  • Export Display
  • DNA Editor Tutorial
• Help Documentation
• Command Line Options

Jemboss is a Graphical User Interface (GUI) to the EMBOSS suite of bioinformatics applications. It is easy to select the most appropriate program and apply the correct selection of options to ensure the best analysis of your biological data.

The following will guide you through a variety of Jemboss uses, from retrieval of a database sequence to exporting a graphical display of your data to a publication manuscript. Small practice sessions at the end of each section of the guide offer examples to help you to make the most of your BioBind software. They are accessible through a cartoon icon.

If you have purchased your bioinformatics analysis package from BioBind, you will be using Jemboss in standalone mode. In this case, all the EMBOSS programs will be installed on your computer. If you have a BioBind installation on a server in your institute, your analyses will be processed on this machine and sent back to your screen in client-server mode.

Standalone Jemboss runs the applications on your own machine. Results are automatically saved in the directory Jemboss is launched from. If you do not change the output file names for an application then they will be overwritten when the analysis is repeated. The output file names can be specified in the interface or changed using the file manager.

Results of any Jemboss analyses run in client-server mode are saved automatically to the server named after the program they were run as and the date and time of the analysis.

The Local Directory path represents the exact location of any file on your computer. Thus files may be accessed using this information at any time without Jemboss.

All files and folders in the local directory are displayed vertically in alphabetical order, much as they would be in other file management applications. Folders may be opened by clicking either on them, or the magnifying glass icon to the left of them. A text file may be edited by double clicking with the left hand mouse button on the filename. After editing, the file may be saved under the same, or a different filename. Picture files (with the suffix .jpeg, .gif or .png) and web files (with the suffix .html) can all be opened from the file manager by double clicking on them.

The three icons above the main file manager allow you to roam across the directories on your local computer.

	Move up one directory
	Move to Working Directory (This is the directory from which you launched Jemboss. If the software was installed from the disc onto a PC, this will be a Cygwin Directory. If Jemboss was launched from a web server, this will likely be the desktop)
	Move to the local home directory. This is generally the one in current use.

A pop-up menu may be accessed by a single right hand mouse button click on the on the file manager. The file manager may be refreshed, and files renamed or deleted by selecting a file and then the appropriate option. A new folder may also be added to the existing data. In this case it is first necessary to highlight the directory in which you wish to create your new folder.

The client-server version of the software also allows access to a remote file manager. This is accessed through the File menu on the Jemboss toolbar as Local and Remote Files. Function is similar to the local file manager, and files may be dropped and dragged between the two locations.

On the left hand side of the interface, EMBOSS programs are categorised into menus based their type of analysis. Clicking on one of these menu buttons will display subcategory menus which lead to the EMBOSS applications. As EMBOSS has been designed to provide programs to satisfy a diverse array of biological analyses, there are over 200 different applications and each of them has a name. In order to assist you in retrieving the correct program for your needs, a short one line description is displayed next to each of these names in the category menus.

Below these categories, the programs are also listed in alphabetical order in a scroll pane. This window is linked to the Go To field just above it, in which the name of the required application may be typed. Programs are highlighted in the scroll menu on typing of the first unambiguous letter of their name. They may then be selected by clicking on them once with the left mouse button or by pressing return. This is a particularly useful option if you use a program frequently.

The Favourites menu is designed to provide shortcuts to those programs most regularly used and to add your own favourites. When a favourite is selected the program form appears. This list may be customised by adding your own commonly used applications. The list of favourites are maintained between Jemboss sessions.

Use the Keyword Search option under the scroll pane to search for a program suited to your analysis. A single or multiple keywords will bring up a list of related programs and a link to their documentation. Use partial keywords to specify your selection more rigidly. Then to select the appropriate analysis, type the application name into the Go To field and retrieve the program form.

The program form for any selected application appears in the main panel. The program name is shown in red at the top of the form, followed by the short description of its function. All the parameters necessary for the correct functionality of the program are available to you in this panel.

File Input

• Directly from the database

Sequences can be analysed directly from the database they are stored in. Hit the Input Sequence Options button below the input field and select the appropriate database from those available. This will automatically input the correct database followed by a colon. The accession number or identifier of the database entry should be typed in this field after the colon (e.g embl:hsfau).

• Drag and Drop

If your sequence files are saved onto your computer, then you can drag them from the local or remote file managers and drop them into the input field. This automatically provides the entire path of the file so it can be analysed by the application.

• Browse

An alternative method of selecting a file for input is to use the Browse button which will allow you to search up and down your other folders for it.

• Cut and Paste

This option allows you to cut and paste your sequence. So if you have output from an analysis done on a web server you can cut and paste it into the Jemboss program form. Simply select the Paste option above the input field and then use Ctl V (hold the control key down whilst also holding the V key down) to paste it into the input box.

• Multiple Files

This option is used to input multiple sequences for example to carry out a multiple sequence alignments. Should all sequences you wish to align not be in the same file, it is possible to select the list of files option and enter each sequence individually. These may be entered directly from the database, or using the drag and drop, or browse options. There is a limit of 20 input fields, but there is no constraint on the type of sequence file (multiple sequence, list, single sequence) or formats that may be entered.

Jemboss reads and writes 42 different types of file format, however the program will automatically determine in what format the input sequence is, so it does not have to be specfied. The exceptions to this are the raw and Intelligenetics formats.

File Output

Should you wish to alter the format of a sequence input, this can be done in the Output Sequence Options. Choose the type of output you would like from the selection in the pull down menu. The result will appear in this format. The default format for all files is fasta format.

Run Parameters

If the parameter input has a range of options, the minimum and maximum values will be displayed in blue together with the default. Some input boxes have a pull down menu below them. In this case, the default option is detailed in the help documentation. If an option from the pull down menu is selected, it will automatically appear in the parameter input box.

If you do not understand the significance of a parameter option, use the mouse over facility to see of there is extra help available. If there is, information will appear on screen in a purple box.

Load Sequence Attributes

Where this option is available, it should be deployed for each sequence used.

Advanced Options

Those parameters not relevant to a particular analysis are greyed out and the input box no longer accessible.

Launch Mode

• Interactive Mode is set as default for the faster analysis programs. In this mode, the Jemboss interface will be halted for the duration of the analysis and the results window will appear automatically on the screen after the analysis is complete. This mode should be selected when the analysis is expected to proceed rapidly.
• Batch Mode is set by default for those applications expected to take a little longer and the analysis is sent to a job manager. This also means that the Jemboss window is not briefly halted and further analyses can be processed. The results window does not appear automatically on the client-server version, and instead must be accessed through the job manager.

The mode may be user defined and should the analysis in question involve a large sequence or search, then it is wise to select batch mode irrespective of what the default for the program may be.

Running the Application

Should the program run not have been successful, a tab displaying an error message will appear in the window. If there is no error message, but there is no results tab, it is likely that something has gone wrong with the input files, and the application could not run.

Type the filename you wish to save your results as into the appropriate field. All files that do not contain a graphic are saved as text files. Text files, therefore, may be appended with any extension, but Jemboss graphics must be saved with the extension .png to allow them to be recognised later. Once you have saved a file, the local file manager with automatically update, to show your new file.

The "save" window defaults to a display of files with the suffixes .fasta; .msf; .gcg; .embl; .swiss. Should your file have a different extension, it will not be displayed immediately, and you will need to alter the Files of Type menu to read "All Files". Graphics files with the extension .png may be viewed both in the Jemboss interface and also in your web browser.

The client-server version of the software also includes the option of saving the results file to the server if the program has been run in batch mode. There are no options to name the file and it is saved to your designated home directory on the server. These results may be accessed using the Saved Results option from the File menu on the Jemboss toolbar.

To accompany these files on the server, the client-server version also offers an option to store information along with the results. The Edit Notes selection on the remote results manager presents the user with a blank note pad on which details of experiments and analyses can be written. This can be saved to the server, and is automatically stored with the results of the relevant analysis.

The Notes may also be saved to the local computer, however this separates them from analysis results and thus they should be named with care.

Add Sequences

Remove Sequences

Sequence Parameters

In the event that only a portion of sequence is required for input, the start and ends points for analysis can be specified. Alternatively, these positions can be calculated for any added sequence by selecting the Calculate Sequence Attributes option from the Tools menu.

Alternatively, if an alignment is output in one of the two formats specified above, the alignment editor can be accessed directly from the results.

Editing Alignments

The alignment may be edited by dragging sequence residues to the right using the mouse with the left hand button depresssed, to create manual insertions. Individual sequences can be locked together using the Lock button at the bottom left hand corner of the editor. Once the sequences are locked, the button becomes an Unlock option for separating the sequences after the edits have been made.

Residues can also be moved to the left providing there is a space created for them by a manual insertion. This allows any mistakes to be rectified, or residue positions to be altered in the light of any additional annotation information.

Should an alignment concern a specific area of the sequence, and this was not specifed as an input option when the alignment was calculated, or to tidy up the N or C termini, sequences can be trimmed in the editor. Select the Trim Sequences option from the Edit menu. All sequences will be trimmed accordingly whether they have been selected or not, and currently this process is not immediately reversible. To reverse this process, the alignment must be closed and the longer length alignment loaded back in.

Calculating Consensus and Identity

The Consensus sequence calculates a consensus for the entire alignment based on the default options of a minimum positive match score of 1.5. In additon, any position scoring at least 1.5 from the default identity matrix will be displayed as a captial letter. These defaults may be altered by setting Set Consensus Options. Threshold options may be set to zero and a Minimum number of identities value may be used instead.

By default the consensus calculations are worked out using the default matrix Blosum62. This can be altered by selecting Matrix Display from the View menu and setting your preferred matrix. The matrix in current use is displayed on the bottom left of the alignment editor window.

Display Options

Alternatively sequences can be coloured based on the number of identities and positive matches in a column. This is the Colour Identical/Matches option under the View menu. The positive matches are defined by the scoring matrix selected. Define the number of identities that are required in a column for them to be set to a given colour with the Identity Number. The default is the maximum number of sequences - i.e. residues that could be conserved in one position. A threshold for positive matches can be set together with, or independently of the identity number. Set the colour options for each of these matches and decide whether the display should be boxed in.

Save Alignment

The consensus sequence can be saved out separately to the alignment. This is saved by default as a fasta formatted file and may be used as input into other applications.

Export Display

To Print the alignment follow the Print Postscript option from the File menu and Print submenu. Your default printer will be accessed and print options are the same as with any other application. Just prior to printing, you will be asked to specify the maximum number of residues that should be displayed on the page. The default is the absolute maximum for the page set up.

To export the display as an png or a jpeg image, follow the same menu but select Print Image Files. Depending on the size of the alignment in question, this may have to be displayed over several files. Select the paper type as would be the case for any print options. Then select the type of image file, maximum number of residues and complete the File Prefix path by adding your chosen filename to the end of it.

Before printing an image, the final display may be previewed. This offers the option to go directly to the Print menu.

The DNA Wizard is set to display the sequence in a circular fashion and it will default to this behaviour each time it is accessed. Thus if you are editing a linear sequence, ensure that this option is selected every time you make an edit using the wizard. Confirm an edit choice by hitting the enter key. Alterations are seen immediately on the display graphic.

Accurate reproduction of sequence features can be done succssfully by inputting the information from a database entry feature table such as EMBL. Alternatively, EMBOSS programs for retrieving ORFs and restriction maps may be run alonside the editor to gain accurate information such as the location of an open reading frame or restriction sites. The editor is not dependent on an actual sequence. Thus the graphical representation offered by the editor may be extended to protein sequences and their relevant features.

Zoom in and out using the View menu to home in on smaller features.

Should the lines look less sharp than you would like, try altering the line width - thinner lines are more defined. The resulting print out should have greater definition than the on-screen view. The resolution of the computer monitor will also affect the view on screen.

Display Attributes

The Tick Marks option allows definition of the numbered markers around or along the display as major and minor ticks. The start site of the markers is also user defined, although the default start site is 0. Ticks can be as frequent as is necessary for the display.

Genetic Markers

To show the direction of the feature, select an arrowhead to point to the right or left. If no direction is attributed to the feature, deselect the arrowhead option. Feature positions may be entered into the relevant field and the associated label can then be edited. Arrowheads can be attributed to marker regions to indicate the way in which they are transcribed. Confirm each choice with the Enter key.

To remove a feature, select the relevant entry and Delete selected row from the Tools menu.

Once the feature is visible on the display, it can be moved in or out of a circular display using the left hand mouse button and dragging the feature to the required position. The graphic size will automatically alter to represent the specified position of the feature.

Restriction Enzymes

Export Display

If you do not require the full documentation, then Parameter help, via tooltips is a quick and easy option to get help on various parameters used within each analysis application. Hover over the parameter name with your mouse and a purple box will appear with the requisite information.

setenv CLASSPATH Jemboss.jar:jakarta-regexp-1.2.jar:JembossPrintAlignment.jarjava org/ emboss/jemboss/editor/AlignJFrame file [options]

The editor will only accept multiple sequence alignment files in fasta or MSF format.  

-calc Calculate consensus and display under the alignment. The following 3 flags can be used to define values used in the calculations.

-plu (plurality) minimum positive match score value for there to be a consensus.

-numid minimum number of identities for there to be a consensus.

-case minimum positive match score for setting the consensus to upper-case.

-color Used to define a colour scheme, below is the list of available colour schemes: taylor residue rasmol acid polar hydrophobic aromatic surface charge size base java org.emboss.jemboss.editor.AlignJFrame file -color size

-font Set the font size.

-id Display a percentage ID pair table.

-noshow Turns of the alignment display.

-nres Number of residues to each line is a print out.

-pretty EMBOSS prettyplot colour scheme. The -matrix flag option can be used to define a scoring matrix for identifying positive matches.

-noBox switch off box drawing around identical and positive matches.

-minID define the minimum number of identities. The default for this is the number of sequences file.

-match define a threshold value for the number of positive matches, the default is half the total wgt.

-colID define a lettering colour for the identities.

-colIDBack define a background colour for identities.

-colMatch define a lettering colour for positive matches.

-colMatchBack define a background colour for positive matches. Available colour options: red, blue, cyan, darkGray, gray , green, lightGray, magenta , orange, pink, white, yellow, black

-print Print the alignment image. The following 2 flags can be used along with the print flag

-prefix prefix for image output file.

-onePage fit the alignment to one page. This option must be be used with the -nres flag to define the residues per line.

-type png or jpeg (default is jpeg).

-antialias turn anti-aliasing on.

-landscape Print as landscape (the default is portrait).

-margin Define the left, right, top and bottom margin (in cm). java org.emboss.jemboss.editor.AlignJFrame file -matrix EBLOSUM62 \ -noshow -print -margin 0.5 0.5 0.5 0.5

-matrix To define a scoring matrix. Used with the -pretty and -calc option.

-list List the available scoring matrix files.

Command Line Examples

java org.emboss.jemboss.editor.AlignJFrame file -matrix EPAM250 \ -pretty -colIDBack black -colID white -print \ -margin 0.5 0.5 0.5 0.0 -noshow