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Comprehensive Overview of EMBOSS Interfaces and Their Functionalities

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21 diapositives · 331 Views · Sep 13, 2014

The EMBOSS (European Molecular Biology Open Software Suite) provides a range of interfaces, including web-based tools like W2H and PISE, as well as character-based and X-Windows interfaces. These interfaces allow users to analyze biological data efficiently. The W2H interface, designed by DKFZ, offers both simple and advanced modes, facilitating program selection and result viewing. Meanwhile, tools like Spin and Kaptain provide graphical outputs suitable for complex analyses. Explore the multitude of EMBOSS interfaces and learn how to maximize their utility for bioinformatics research.

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  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’

  21. THE END