Comprehensive Overview of EMBOSS Interfaces and Their Functionalities

1. EMBOSSINTERFACES Gary Williams

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

3. Web interface details • Many are being developed: • W2H (http://www.hgmp.mrc.ac.uk/Registered/Webapp/emboss-w2h/) • celbalo (http://corba.ebi.ac.uk/cgi-bin/alweb2/alweb.start?CFG=Emboss) • PBI interface (http://bioinfo.pbi.nrc.ca:8090/emboss/index.html) • Pise (http://ubigcg.mdh4.mdc-berlin.de:8080/) • Pise details (http://www-alt.pasteur.fr/~letondal/Pise/) • wEMBOSS (http://sol.biol.unlp.edu.ar/cgi-bin/embnet/wEMBOSS) • wEMBOSS details (http://sol.biol.unlp.edu.ar/wEMBOSS)

4. 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/)

5. Character menu interface • Only one: • emnu

6. We will be looking at these • Spin - X-Windows interface • W2H - Web interface • emnu - character menu interface

7. 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

8. 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

9. 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

10. 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

11. emnu - Practical • Display the available databases (showdb) • Compare embl:hsfau and embl:hsfau1 using: • dottup with a wordsize of 10 • est2genome • Translate embl:hsfau using ‘transeq -regions’ • Use the previous comparisons to get the regions to translate • Or use ‘showfeat -pos’ • Or use ‘entret’

12. 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.

13. 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.

14. 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

15. 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

16. 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:’

17. W2H - Practical • Compare ‘embl:hsfau’ and ‘embl:hsfau1’ using: • est2genome (note strange position of genomic sequence prompt) • water (note the wrong position of the second file prompt) • Plot the charges along ‘sw:100k_rat’ using ‘charge’ (click on the ‘Produce graphic’ button)

18. 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.

19. 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

20. spin - Practical • Plot the curvature of ‘embl:hsfau’ using ‘banana’ • Find all occurrences of ‘GACT’ in ‘embl:hsfau’

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