EMBOSS INTERFACES

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EMBOSSINTERFACES

• Gary Williams

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Interfaces

• Web
• EMBOSS W2H
• PISE
• wEMBOSS
• celbalo
• PBI
• X-Windows
• GCG - Seqlab
• EMBOSS - SPIN, ( others coming)
• Telnet/xterm/Character-based
• emnu

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Web interface details

• Many are being developed
• W2H (http//www.hgmp.mrc.ac.uk/Registered/Webapp/e
  mboss-w2h/)
• celbalo (http//corba.ebi.ac.uk/cgi-bin/alweb2/alw
  eb.start?CFGEmboss)
• PBI interface (http//bioinfo.pbi.nrc.ca8090/embo
  ss/index.html)
• Pise (http//ubigcg.mdh4.mdc-berlin.de8080/)
• Pise details (http//www-alt.pasteur.fr/letondal/
  Pise/)
• wEMBOSS (http//sol.biol.unlp.edu.ar/cgi-bin/embne
  t/wEMBOSS)
• wEMBOSS details (http//sol.biol.unlp.edu.ar/wEMBO
  SS)

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X-Windows interfaces

• At least three are being developed
• Spin (Staden package)
• Kaptain (http//userpage.fu-berlin.de/sgmd/)
• Arka (http//www.bioinformatics.org/genpak/)

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Character menu interface

• Only one
• emnu

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We will be looking at these

• Spin - X-Windows interface
• W2H - Web interface
• emnu - character menu interface

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emnu

• Type emnu at the Unix prompt
• Menu of program groups is shown
• Can move up and down using arrow keys
• Can move to an option by typing first characters
• Can move by typing U/D (up/down) ...
• or P/Z (page up/page down)
• Can select by pressing RETURN
• Can select by double-clicking on an option
• Or you can type ANY Unix command

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emnu - programs menu

• Selecting a group gives the programs menu
• Move around the menu as before
• Type ? to get help on the current program
• Can edit the line displaying the current program
• e.g. E to get to the end, then type -opt
• Press RETURN to start the program
• from now on the menu has no effect
• the program takes over, prompting for any
  required
• data and displaying graphics.
• more new-files is now the default command

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emnu - files menus

• At any time you can type T (files) or N
  (newfiles)
• You see Name, (Dir), Date Time, Size
• Selecting a directory moves into it
• Selecting a file displays it using more
• Other things
• F1 - view, F2 - sequence, F3 copy, F5 delete
• The last used file becomes the default for those
  keys after leaving this menu
• F4 - new dir, F8,F9 - sort by name,time

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emnu - Command line editing

• Emnu is just a menu on top of the command-line
• You can enter any command you like for Unix
• Edit the command line using
• F - forward, B - back, A - start, E - end
• C - delete line, K - delete to end of line
• R - recall stored file, G - recall default file
• TAB - fill out rest of current menu option

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emnu - Practical

• Display the available databases (showdb)
• Compare emblhsfau and emblhsfau1 using
• dottup with a wordsize of 10
• est2genome
• Translate emblhsfau using transeq -regions
• Use the previous comparisons to get the regions
  to translate
• Or use showfeat -pos
• Or use entret

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W2H

• Developed by DKFZ for Hussar and GCG
• EMBOSS works under it with little change
• The demo tutorial is still written for GCG!
• Go to web page
• http//www.hgmp.mrc.ac.uk/Registered/Webapp/emboss
  -w2h/
• Simple mode/advanced mode - choose simple
• Have buttons for pages main, results, files, etc.

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W2H - Main page

• Menu of programs to select
• Fields to paste/upload/select sequence to analyse
• Click on the red Start button to run the
  program
• Form for options appears - click on Run button
• Output to screen appears.

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W2H - Results page

• Shows results from W2H programs
• Refreshed every 10 seconds
• Application link shows command that was run
• Output file link gives output files

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W2H - Files page

• Displays files (with selection mask)
• Click on directory to enter
• Click on file to view it
• Other button do things to selected files
• Delete
• Copy
• Rename
• Make Dir

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W2H - oddity

• When some programs expect to read in two files
  (e.g. water), the second file is prompted for in
  the Optional parameters section with just the
  prompt File Using

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W2H - Practical

• Compare emblhsfau and emblhsfau1 using
• est2genome (note strange position of genomic
  sequence prompt)
• water (note the wrong position of the second file
  prompt)
• Plot the charges along sw100k_rat using
  charge (click on the Produce graphic button)

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SPIN

• Written by the Staden team
• Not part of the Staden package, but shares their
  look feel
• Requires an X-Windows interface
• Still in beta-testing phase
• Type spin in EMBOSS option.

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spin - main interface

• Before anything else, you must load a sequence
• File Load sequence
• Click on the Emboss menu to select a program
• The results appear in the Output Window as well
  as in a file
• Currently the Help option describes the Staden
  package!
• Graphical output (e.g. dottup) is displayed in a
  zoomable interface

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spin - Practical

• Plot the curvature of emblhsfau using banana
• Find all occurrences of GACT in emblhsfau

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THE END