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cgi-bin
conf
lib
sample_query_sequence
CREDITS
DISCLAIMER
MANIFEST
Makefile.PL
README
VERSION

README

This is a fork of the orginal BLAST Graphics Viewer used in LiceBase (licebase.org).
We have attempted to update the code and fix issues where it was slightly broken or out of date.

We have also changed and added some features:
 
 - supports only NCBI Blast+ (not WU-blast any more) binaries and options (icluding "Task" parameter)
 - added support for SAML authentication and logins via Net::SAML module
 - this change required to add full session management using CGI::Session
 - changed the configuration file parser to Config::IniFiles to allow for more refined blast database configuration, that also means the config files need to be changed, look at example.conf
 - primary links can now be set in the configuration DB stanza
 - GBrowse URLs can now be configured via the configuraton file for each database, they appear below the Blast HSP entry on the result page
 - all URL parameters are now filtered through String::ShellQuote
 - script remembers settings for sequence, program, Task, and blast db 
 - these parameters can also be controlled by URL: nph-blast.pl?program=blastn&task=blastn-short 
 - added our own HTML writer module because we need to be able to configure the output to enable these features
 - added a mechanism that can connect to a CHADO backend to retrieve sequence files
 - added a mechanism that can write a feature location entry derived from BLAST coordinates
   to CHADO for sequences retrieve from CHADO
 - script reads the location of the CSS file from the configuration
 - script can be called with embedd=1 parameter, then the script will not display greetings, title, and login and logout information
 - put the image generation in an eval
 - 'fixed' anchor links between graphics and textual result, works now but only for Nucleotide sequences  

TODOs:
 - fix hyperlinks between graphics and textual result for non DNA
 - remove all remnants of outdated WU-blast, in favor of open-source NCBI blast
 - the original 'synchroneous job handling' is naively implemented. 
   * result page can time out
   * no wait indicator
   * no job management, easy to overload server
   -> implement result page in Ajax with 'spinner'
   -> integrate one/many proper queueing system, e.g. OGE via DRMAA
 - allow for more than a single query sequence


================================= Original README =============================================

The BLAST Graphic Viewer provides a graphical visualization of the regions 
contained within HSPs relative to the query sequence. This distribution 
includes sample databases and a BLAST Search form. It is a component of 
the Generic Model Organism Systems Database project (GMOD.sourceforge.net).

 - For a demo, go to http://seq.yeastgenome.org/cgi-bin/GMOD/nph-blast.pl
 
 - To download the Washington University BLAST(WU-BLAST), 
   go to http://blast.wustl.edu/

 - To download the BLAT programs, 
   go to http://www.genomeblat.com/genomeblat/

 - To download the NCBI BLAST programs, 
   go to http://www.ncbi.nlm.nih.gov/BLAST/
 
 - To download the sample databases, go to 
   ftp://genome-ftp.stanford.edu/pub/people/programmer/gmod/

 - This graphic module will support BLASTN, BLASTP, BLASTX, TBLASTX, 
   TBLASTN, BLAT, and TBLATN. For the databases, it will support any fasta-
   formated datasets (i.e., nr, nt, etc). 

 - The cgi program (nph-blast.pl) included in this
   distribution is used to display a BLAST/BLAT search form and 
   search result for WU-BLAST or BLAT. It can be copied into any directory 
   under your cgi-bin. You can update the $CONF_FILE variable 
   in the top of this script to point to your own location of 
   the configuration file.

 - To set your own locations for blast programs, databases, filters,
   and matrix, and tmp directory for storing the png file, please 
   see the configuration file (conf/Blast.conf). You can copy this 
   file (Blast.conf) into any world readable directories.

 - To install this module on your own system, issue the following commands:

   perl Makefile.PL
   make
   make install   

 - Prerequisites: this module runs on top of several software packages. 
   These packages must be installed before you can run this viewer. 

	A)  	Apache Web Server -- http://www.apache.org
        		The Apache web server is the industry 
			standard open source
        		web server for Unix and Windows systems.

  	B) 	Perl 5.005 or higher-- http://www.cpan.org
        		The Perl language is widely used for web 
			applications.
        	
  	C)	Standard Perl modules -- http://www.cpan.org
        		The following Perl modules must be installed 
			for the Blast Graphic Viewer to work.
        		They can be found on CPAN:

		File::Listing
		File::Basename
		GD
		CGI
		

	D)	Bioperl modules --  http://www.bioperl.org
        		The following Bioperl modules must be installed
			for this viewer to work.	
	
		Bio::Root::IO
		Bio::SearchIO
		Bio::SearchIO::Writer::HTMLResultWriter
	

This is a free software. You can use it under the same terms as Perl
itself. Please see DISCLAIMER for limitations ...
 	
Support is available from the discussion groups and mailing lists at
www.gmod.org

Shuai Weng & SGD team
shuai@genome.stanford.edu
www.yeastgenome.org
Nov. 15, 2005