EMBOSS INTERFACES Gary Williams Interfaces n Web u
EMBOSS INTERFACES Gary Williams
Interfaces n Web u EMBOSS W 2 H u PISE u w. EMBOSS u celbalo u PBI n X-Windows u GCG - Seqlab u EMBOSS - SPIN, (+ others coming) n Telnet/xterm/Character-based u emnu
Web interface details n Many are being developed: W 2 H (http: //www. hgmp. mrc. ac. uk/Registered/Webapp/embossw 2 h/) u celbalo (http: //corba. ebi. ac. uk/cgibin/alweb 2/alweb. start? CFG=Emboss) u PBI interface (http: //bioinfo. pbi. nrc. ca: 8090/emboss/index. html) u Pise (http: //ubigcg. mdh 4. mdc-berlin. de: 8080/) u Pise details (http: //www-alt. pasteur. fr/~letondal/Pise/) u w. EMBOSS (http: //sol. biol. unlp. edu. ar/cgibin/embnet/w. EMBOSS) u w. EMBOSS details (http: //sol. biol. unlp. edu. ar/w. EMBOSS) u
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/)
Character menu interface n Only one: u emnu
We will be looking at these n n n Spin - X-Windows interface W 2 H - Web interface emnu - character menu interface
emnu n n n n n 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
emnu - programs menu n n n 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 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
emnu - files menus n n n 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: u F 1 - view, F 2 - sequence, F 3 copy, F 5 delete u The last used file becomes the default for those keys after leaving this menu u F 4 - new dir, F 8, F 9 - sort by name, time
emnu - Command line editing n n n 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: 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
emnu - Practical n n Display the available databases (showdb) Compare embl: hsfau and embl: hsfau 1 using: u dottup with a wordsize of 10 u est 2 genome 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’
W 2 H n n 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: u n n http: //www. hgmp. mrc. ac. uk/Registered/Webapp/emboss-w 2 h/ Simple mode/advanced mode - choose simple Have buttons for pages: main, results, files, etc.
W 2 H - Main page n n n 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.
W 2 H - Results page n n Shows results from W 2 H programs Refreshed every 10 seconds Application link shows command that was run Output file link gives output files
W 2 H - Files page n n Displays files (with selection mask) Click on directory to enter Click on file to view it Other button do things to selected files: u Delete u Copy u Rename u Make Dir
W 2 H - 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: ’
W 2 H - Practical n Compare ‘embl: hsfau’ and ‘embl: hsfau 1’ using: u est 2 genome (note strange position of genomic sequence prompt) u water (note the wrong position of the second file prompt) n Plot the charges along ‘sw: 100 k_rat’ using ‘charge’ (click on the ‘Produce graphic’ button)
SPIN n n n 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.
spin - main interface n Before anything else, you must load a sequence u File: n n 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
spin - Practical n n Plot the curvature of ‘embl: hsfau’ using ‘banana’ Find all occurrences of ‘GACT’ in ‘embl: hsfau’
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