EMBOSS INTERFACES Gary Williams. Interfaces n Web u EMBOSS W2H u PISE u wEMBOSS u celbalo u PBI n X-Windows u GCG - Seqlab u EMBOSS - SPIN, (+ others.

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’

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