EMBOSS INTERFACES
description
Transcript of EMBOSS INTERFACES
EMBOSSINTERFACES
Gary Williams
Interfaces
Web EMBOSS W2H PISE wEMBOSS celbalo PBI
X-Windows GCG - Seqlab EMBOSS - SPIN, (+ others coming)
Telnet/xterm/Character-based emnu
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)
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/)
Character menu interface
Only one: emnu
We will be looking at these
Spin - X-Windows interface W2H - Web interface emnu - character menu interface
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
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
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
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
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’
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.
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.
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
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
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:’
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)
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.
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
spin - Practical
Plot the curvature of ‘embl:hsfau’ using ‘banana’ Find all occurrences of ‘GACT’ in ‘embl:hsfau’
THE END