Wscope

Ripp — Thu, 09 Sep 2010 10:11:23 GMT

New page

Wscope is the web interface of [[Gscope]]

It runs as cgi-bin and has access to almost all procedures of Gscope

http://lbgi.igbmc.fr/gag/cgi-bin/GscopeServer?Science&Command&arg1&arg2 (Science is a Gscope Project, Command a procedure)

* http://lbgi.igbmc.fr/gag/cgi-bin/GscopeServer lists all existing projects are listed
* http://lbgi.igbmc.fr/gag/cgi-bin/GscopeServer&Science gives access to a guide (GuideMoi)
* http://lbgi.igbmc.fr/gag/cgi-bin/GscopeServer&Science&FileMoi&BOX001 gives access to all information concerning BOX001 (FileMoi)
* http://lbgi.igbmc.fr/gag/cgi-bin/GscopeServer&Science&FicheMoi lists all summary files from directory fiches (FicheMoi)
* http://lbgi.igbmc.fr/gag/cgi-bin/GscopeServer&Science&RechercheMoi allow textual or blast searching (RechercheMoi)

==GuideMoi==
The most common possible actions are listed BUT

The owner of the Gscope Project can add specific actions for his project by creating the file '''fiches/WscopeLinksGuideMoi.txt''' as for example : (notice the use of [WscopeScience] or LbgiUrl] or [PreFixe], etc)

<source lang=tcl>
#put here the link and the text todispaly (separated by as many tabulations as you want, at least 1)
# line starting with # are skiped
# empty link and/or text are allowed
#Link Texte

[LbgiUrl]/MeltingTemperatureBioPhp.php Calculate Melting Temperature
[WscopeScience]&Signal All Signals
[WscopeScience]&BrocOli&AllHtml BrocOli ( Broken Oligos = generic oligos )
[WscopeScience]&ShowRestrictionEnzyme Restriction Enzymes
[WscopeScience]&RestrictionEnzymesStatistics&ShowStatistics ... their Statistics
[WscopeScience]&RestrictionEnzymesStatistics&ShowHits ... their Hits
[WscopeScience]&AffichePof&AllPs All existing oligos
[WscopeScience]&AfficheVirtualPPCR All PCR products
[WscopeScience]&AfficheLesRec1 All Rec1 (ie pDONR)
[WscopeScience]&AfficheLesRec2 All Rec2 (ie pDEST)
[WscopeScience]&SpineSummaryOnWeb Spine Targets Summary
[WscopeScience]&OliWeb Order oligos (not yet available)
</source>

==FileMoi==
As for GuideMoi the owner can add specific actions for his BOXes by creating the file '''fiches/WscopeLinksFileMoi.txt''' (notice the use of $Qui or [Alias $Qui])

<source lang=tcl>
#rR WscopeLinksFileMoi.txt
#Ref Text
[WscopeServer]?ProGS&ShowCloning&$Qui Show Cloning=All about oligos, PCR products, Recombinaison, etc.
[WscopeServer]?ProGS&CheckRestrictionEnzymes&$Qui&All RestrictionEnzymes=Check Restriction Enzymes for $Qui
[WscopeServer]?ProGS&FileMoi&infos&$Qui SeqCheck=See your sequence checking and other infos
[LbgiUrl]/wikili/index.php/Gscope_Clonage Wiki Gscope=Tout ce que vous aimeriez connaitre sur Gscope Clonage
</source>

==RechercheMoi==
A textual search is done in all infos/BOXxxx files

The Blast search is done in the blast databases found in banques/ (see [[Blast On Gscope Project]])

Blast On Gscope Project

Ripp — Thu, 09 Sep 2010 09:32:47 GMT

New page

Blast Database of a Gscope Project

==How to create it==
Each [[Gscope]] Project has a directory '''RepertoireDuGenome/banques''' where you can find the blast databases concerning the project.

The owner of the project can create as many blast database as he wants.

How to create a blast database (for example all proteins)

cd $RepertoireDuGenome/prottfa
cat * > $RepertoireDuGenome/banques/AllProttfa
cd $RepertoireDuGenome/banques
formatdb -i AllProttfa -p T

this can be done by

gscope CreeUneBanqueBlast AllProttfa

Attention ! if somebody uses [[Wscope]] (Gscope on the Web) the first available database will be choosen as default database, so the alphabetic order is important (anyway, the user can check what he wants ...)

==How to use it==

blastall -p blasp -i YourInputFasta.tfa -o YourOutputFile.blast -d $RepertoireDuGenome/banques/AllProttfa

and ... on the web, the fommular appears when you do a search.

http://www-bio3d-igbmc.u-strasbg.fr/~ripp/cgi-bin/gscope_html_server.tcsh?ProGS&RechercheMoi

==Database not available==

If you are on the web and no database appears, please ask the owner of the database to create it, or mail to Raymond.

Wikili - Recent changes [en]

Wscope

Blast On Gscope Project