You need to download and unpack both gepis_scripts.tar.gz and gepis_data.tar.gz 
to make the program work.


gepis_scripts.tar.gz is packed with Perl scripts, expect scripts and a C program 
needed for GEPIS analysis. To run the program on your system, please read the 
README file in gepis_scripts.tar.gz for instructions.


gepis_data.tar.gz has all the sequence databases, library files and precomputed 
results needed for GEPIS analysis. 


***ATTENTION:***
you need to download and unpack gepis_data.tar.gz before you run the configuration 
script in gepis_scripts.tar.gz !!

 


==================Files packed into gepis_scripts.tar.gz=====================================================

***Expect script***
HsDataDL.exp			ftp Hs_LibData.dat from  ftp://ftp1.nci.nih.gov/pub/CGAP/
nci-cancer.exp			retrieve cancer EST library information from cgap.nci.nih.gov 
nci-nomral.exp			retrieve normal EST library information from cgap.nci.nih.gov 
ncbi.exp			ftp LL_tmpl.gz, seq_gene.md.gz and ideogram.gz from 
				ftp.ncbi.nih.gov
	                	LL_tmpl:the locus link template file 
		     		seq_gene.md:information about CDSs, UTRs and genes in contigs. 
		     		ideogram:cytoband data	



***perl scripts****

NOTE: type "XXX.pl -h" to get help information for most perl scripts.


***EST library file construction***
gepisLibPrepWrapper.pl		call  HsDataDL.exp, nci-cancer.exp, nci-nomral.exp, nciDlCleaser.pl, 
				pre_prepareLib4gepisDELNCI.pl, and prepareLib4gepisDELNCI.pl in
				turn to download and compile library files used in GEPIS analysis. 
				Run it to get latest EST library information.
nciDlCleaser.pl			get rid of header in the downloaded file
pre_prepareLib4gepisDELNCI.pl	cleanse downloaded EST library information
prepareLib4gepisDELNCI.pl	compile the library files used in GEPIS analysis 


***GEPIS Analysis on single sequence***
gepisFromFastaFile.pl		perform GEPIS analysis on input fasta file (one sequence at a time)


***Mining GEPIS result***
gepisMiningWrapper.pl		calls the following perl scripts in turn to carry out tissue-specificity 
				and tumor-antigen mining for a given sequence collection


preComputeGepisAnalysis.pl	perform GEPIS analysis on input multiple sequence fasta file. It calls 
				gepisFromFastaFile.pl sequentially for each sequence. Can be 
				modified to run gepisFromFastaFile.pl in parallel.
gepisDataCollector.pl		collect the gepis analysis data to compile a data file
gepisProfile.pl			collect the stats on expression data, the median DEL leve l of normal 
 				is used as a parameter in further mining process
tsFinder.pl 			mine tissue-specific records
heatMap.pl 			graphic display of  tissue-specific records
taPicker.pl			mine tumor-antigen-candidates
heatMapForTA.pl			graphic display of tumor-antigen-candidates



***download LocusLink files and build LocusLink sequence database ***
buildLocusLinkSeqDB.pl		call ncbi.exp to download files and parseNCBIcb.pl to parse out the start, 
				end and centromere postions of each chromosome.  Build LocusLink sequence 
				db and extract genomic coordinates from download files.
					
				NOTE: this file is not ready to deploy and sequence retrieval method have 
				to be implemented by usr. Please read the source code for implementation
				detail.

parseNCBIcb.pl			read downloaded ideogram file and parse out the start, end and centromere
				postions of each chromosome. 



***retrieve genomic coords and find neighboring genes ***
chrLocServer.pl			server process
chrLocClient.pl			client process



***web interface***
web_searchinput.pl		web search interface
web_search.pl			running Gepis Analysis for web query sequence
web_draw.pl			drawing program
web_drawcharts.pl		drawing program
web_toexcel.pl			export the Gepis result into excel sheet

All the web_xxx scripts should to be deployed into a cgi dir under  document root.



***Modules***
gepisChart.pm			routines for drawing diagrams and charts:
				e.g:	tissue-profiling and Regional Gepis Atlas

GD/Graph/DNA	
				Karyotype.pm    area.pm         axestype.pm     
				bars.pm         errorBars.pm    lines.pm        
				linespoints.pm  multiLabels.pm  points.pm       vwbars.pm

	 			extensions of GD/Graph modules for drawing bar, line, 
				points...chart.



***C program***
zstat		 		calculate P value for ztest score




===========================Files packed into gepis_data.tar.gz===============================================

***sequence database***:
db/
hest		 		human EST sequence


***EST library information***
LIB/
nci_libInfo.sn.human			human EST normal and cancer library (non-normalized, 
					non-subtracted) information
organEST-sn.nci.human.sn.usable	 	total EST counts in each tissue category.



***locuslink download***
locuslink/

LL_tmpl				LocusLink template file
seq.locuslink			collection of representative mRNAs of human locuslink entries 
seq.locuslink.id.dat	 	compiled precomputed GEPIS analysis result on sequences of LocusLink records
seq_gene.md			genomic coordinates of LocusLink records
ideogram		 	Karyotype, chromosome Length 


gepis_result/
individual GEPIS analysis result for each LocusLink record 



===================================Reports==================================================================
  
Please  report  bugs  by  e-mail to  `yz5@gene.com' or 'zemin@gene.com'
with a detailed explanation of the  problem.


The Gepis Team