1. EMBOSS INTERFACES Gary Williams

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

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

4. X-Windows interfaces n At least three are being developed: u Spin (Staden package) u Kaptain (http://userpage.fu-berlin.de/~sgmd/) u Arka (http://www.bioinformatics.org/genpak/)

5. Character menu interface n Only one: u emnu

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

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

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

9. emnu - files menus n At any time you can type ^T (files) or ^N (newfiles) n You see Name, (Dir), Date & Time, Size n Selecting a directory moves into it n Selecting a file displays it using ‘more’ n Other things: u F1 - view, F2 - sequence, F3 copy, F5 delete u The last used file becomes the default for those keys after leaving this menu u F4 - new dir, F8,F9 - sort by name,time

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

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

12. W2H n Developed by DKFZ for Hussar and GCG n EMBOSS works under it with little change n The demo tutorial is still written for GCG! n Go to web page: u http://www.hgmp.mrc.ac.uk/Registered/Webapp/emboss-w2h/ n Simple mode/advanced mode - choose simple n Have buttons for pages: main, results, files, etc.

13. W2H - Main page n Menu of programs to select n Fields to paste/upload/select sequence to analyse n Click on the red ‘Start’ button to run the program n Form for options appears - click on ‘Run’ button n Output to screen appears.

14. W2H - Results page n Shows results from W2H programs n Refreshed every 10 seconds n Application link shows command that was run n Output file link gives output files

15. W2H - Files page n Displays files (with selection mask) n Click on directory to enter n Click on file to view it n Other button do things to selected files: u Delete u Copy u Rename u Make Dir

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

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

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

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

21. THE END