#TDNAExpress Configuration and Data File
#Tabbed for each column

#TITLE of the project
#TITLE	Arabidopsis thaliana [AGI/TAIR V6]
TITLE	Arabidopsis thaliana [TAIR/AGI V7]

#HTTPServer	http://signal.salk.edu
HTTPServer	http://198.202.69.59
#CGIProgram	/cgi-bin/tdnaexpess
CGIProgram	/cgi-bin/atta
#documentRoot directory -- the same as the Apache Server (http://signal.salk.edu)
#DocumentRoot	/export/quantum/webs/htdocs
DocumentRoot	/var/www/html

Port	4040

#graphyTemp directory -- a temporery directory in relative path to put graphic images
#if set to "tmp",  the images will be wroten to /home/gedb/webs/htdocs/tmp direcotry 
#and display as http://signal.salk.edu/tmp.
GraphyTemp	temp
#GraphyTemp	tmp

#List Client machines allowed to access the severlet
#list Allow, Deny: All or Only or File
SearchAllow	All
#SearchAllow	Only	signal.salk.edu
#SearchAllow	File	/etc/hosts

#SearchDeny	All	//except itself and Only allowed
#GraphyDeny	File	/etc/hosts.deny		//default

#logfile to record accesses
#LogFile	/home/gedb/logs/tdnaexpress.log

#Below are examples for CGI sending data to ServerLet. Not parts of the configuration
#Search	SearchString	SaveFile
#Search TDNA=SALK_00002 
#Map	SearchString	
#Map	TDNA=SALK_00002 

#define the image width you send to users, it could be changed by users
ImageWidth	800

#define the default zoom factor, if not set, it is 100
#Zoom is allowed to vary from "minZoom" to "maxZoom".
Zoom	40	//default zoom factor : ( 100 bases/pixel)
MinZoom	1	//Minimum zoom factor allowed
MaxZoom	160	//Maximum zoom factor allowed
ZoomScale	160 100 60 40 20 10 5 1
TilingGeneScale	4  4 4 4 3 3 2 2
TilingTDNAScale	17 17 16 16 15 15 14 14

#Display	Tiling or Track -- Track = True, Tiling = False signal.salk.edu
#Display	Tiling
Display	Track

#DataType	DataName	File	Color
#DataType = Gene, Genome, Expression and Data (cDNA, TDNA, EST, mRNA ... )
#Gene and Others allow links immediately fellow them
#Genome display as a slide bar to seperate gene and the others
#Expression has no links. Expression file allow only one and must define tracks if track mode.

#Expression	"Natural Variation"	expression.txt	00FF00
#MultipleExpression	"Natural Variation"	expression.txt	2	Night	00FF00	Day	FF0000

#define ExpressionDisplayMode, either Tracks, Lines, or Bars
#ExpressionDisplayMode	Track


#Gene	Name	File	Color	Highlight	Annotation
#Gene	Gene	/home/gedb/arab/Feb2004/geneannotation.jul2005.txt	00A300	
#Gene	Gene	/home/gedb/arab/Feb2004/geneannotation.oct2005.tairv6.txt	00A300
GENE	Gene	/home/gedb/arab/Feb2004/geneannotation.Apr2007.tairv7.txt	00A300
TRACK	0	3
SHAPE	ARROW	3
LINK	[<a href=http://signal.salk.edu/cgi-bin/tdnaexpress?JOB=iSECT&EXT5=0&EXT3=0&INCLUDE=0&LIST=$>Seq</a>]
LINK	[<A href=http://signal.salk.edu/cgi-bin/atta?GENE=$>Transcriptome</a>] [<A href=http://signal.salk.edu/cgi-bin/RiceGE?DATA=$>RiceGE</a>]
LINK	[<a href= http://natural.salk.edu/cgi-bin/snp.cgi?CHROMOSOME=$1&COORS=$3>SNP Search</a><img src=/Images/new.gif>]
LINK	[<a href=?JOB=EXPR&TYPE=GPL198&QUERY=$ target=_blank>gAtlas</a><img src=/Images/new.gif>]
LINK	[<A href=http://natural.salk.edu/cgi-bin/gosearch?FIELD=GENE&QUERY=$>GO</a>]
LINK	[<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?SUBMIT=y&db=nucleotide&term=$ target=_blank>NCBI</a>]
LINK	[<a href=http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?chr=arabid.inf&col=8&query=$&sqchr= target=_blank>NCBI Map</a>]
LINK	[<a href=http://arabidopsis.org/servlets/TairObject?type=locus&name=$ target=_blank>TAIR</a>]
LINK	[<a href=http://mips.gsf.de/cgi-bin/proj/thal/search_gene?code=$ target=_blank>MIPS</a>]
LINK	[<a href=http://mpss.udel.edu/at/GeneAnalysis.php?featureName=$ target=_blank>MPSS</a>]
LINK	[<a href=http://www.plantenergy.uwa.edu.au/applications/suba/flatfile.php?id=$ target=_blank>AMPDB/SUBA</a>]
LINK	[<a href=http://www.genome.jp/dbget-bin/www_bget?ath+$ target=_blank>KEGG</a>]
LINK	<br>       [<a href=http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi?db=ath1&orf=$ target=_blank>TIGR</a>]
LINK	[<a href=http://synteny.cnr.berkeley.edu/AtCNS/synteny_pair.pl?action=Find+Syntenic+Pairs+with+Accession&accn=$ target=_blank>Synteny Gene Pairs</a>]
LINK	[<a href=http://jsp.weigelworld.org/expviz/expviz.jsp?experiment=development&normalization=absolute&action=Run&probesetcsv=$ target=_blank>AtGene Express</a>]
LINK	[<a href=http://www.plantgdb.org/AtGDB-cgi/findRegion.pl?id=$ target=_blank>AtGDB View</a>]
LINK	[<a href="http://bbc.botany.utoronto.ca/efp/cgi-bin/efpWeb.cgi?primaryGene=$&modeInput=Absolute" target="_other">e-FP Browser</a>]
LINK	[<a href="http://affymetrix.arabidopsis.info/narrays/digitalnorthern.pl?selection=&arraydesign=-400000&searchfor1=AGI&id1=$" target="_other">NASCArrays Digital Northern</a>]
LINK	<br>       [<a href=http://www.arabidopsis.org/servlets/TairObject?type=clone&name=YE$ target=_blank>YE Clone</a>]
LINK	[<a href="http://affymetrix.arabidopsis.info/narrays/spothistory.pl?selection=no&searchfor=AGI&id=$" target="_other">NASCArrays Spot History</a>]
LINK	[<a href="https://www.genevestigator.ethz.ch/at/index.php?page=tair&option=atlas&agi=$" target="_other">Genevestigator Gene Atlas</a>
LINK	<a href="https://www.genevestigator.ethz.ch/at/index.php?page=tair&option=chrono&agi=$" target="_other">Gene Chronologer</a>
LINK	<a href="https://www.genevestigator.ethz.ch/at/index.php?page=tair&option=stress&agi=$" target="_other">Response Viewer</a>]
LINK	<br>       [<a href=http://signal.salk.edu/cgi-bin/methylome?GENE=$>Methylome</a>]
LINK	[<a href=http://bbc.botany.utoronto.ca/>UToronto BAR</a> <a href=http://bbc.botany.utoronto.ca/ntools/cgi-bin/ntools_expression_angler.cgi>Expression Angler</a>
LINK	<a href=http://bbc.botany.utoronto.ca/ntools/cgi-bin/ntools_expression_angler.cgi?agi_id=$&match_count=25&default_db=NASCArrays>NASCArrays</a>
LINK	<a href=http://bbc.botany.utoronto.ca/ntools/cgi-bin/ntools_expression_angler.cgi?agi_id=$&match_count=25&default_db=BADB>BADB</a>
LINK	<a href=http://bbc.botany.utoronto.ca/ntools/cgi-bin/ntools_expression_angler.cgi?agi_id=$&match_count=25&default_db=AtGenExpress_Hormone_raw>Hormone</a>
LINK	<a href=http://bbc.botany.utoronto.ca/ntools/cgi-bin/ntools_expression_angler.cgi?agi_id=$&match_count=25&default_db=AtGenExpress_Stress_raw>Stress</a>
LINK	<a href=http://bbc.botany.utoronto.ca/ntools/cgi-bin/ntools_expression_angler.cgi?agi_id=$&match_count=25&default_db=AtGenExpress_Pathogen_raw>Pathogen</a>
LINK	<a href=http://bbc.botany.utoronto.ca/ntools/cgi-bin/ntools_expression_angler.cgi?agi_id=$&match_count=25&default_db=AtGenExpress_Tissue_raw>Tissue</a>
LINK	<a href=http://bbc.botany.utoronto.ca/ntools/cgi-bin/ntools_expression_angler.cgi?agi_id=$&match_count=25&default_db=AtGenExpress_Tissue_Plus_raw>Ext Tissue</a>]

#DATA	Type	Name	File	Color
#LINK	URL	//LINK must follow its data
#SHAPE	TYPE	PARAMETER
#SHAPE	LINE	3		//WIDTH
#SHAPE	ARROW	3		//WIDTH
#SHAPE	TRIANGLE	<	//< Left > Right v Down ^ Up
#SHAPE	TRANSCRIPTOME	
#SHAPE	DENSITY			//Greyed
#TRACK	3	3		//Track	Trackno	Trackspan

DATA	TDNA	SALK T-DNA	/home/gedb/arab/Feb2004/salk.tdna.un	EF3399
TRACK	1	9
SHAPE	ARROW	1
OPTION	TEXTON	1-50
#DATA	TDNA	SALK T-DNA	/home/gedb/tdna/salk.tdna	880055	
LINK	[<a href=/cgi-bin/viewfile?web+a+a+jose+$>seq</a>]
LINK	[<a href=http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12893945>About &amp; Citation</a>]
LINK	[<a href=http://signal.salk.edu/tdna_protocols.html>Vector</a>]
LINK	[<a href=/cgi-bin/tdnainfo?TDNA=$>analysis</a>]
LINK	[<a href=http://www.arabidopsis.org/servlets/SeedSearcher?action=detail&stock_number=$ target=_blank>Order from ABRC</a>]
LINK	[<a href= http://arabidopsis.info/MultiResult?name=$>Order from NASC</a>] 

DATA	TDNA	SALK T-DNA HM	/home/gedb/arab/Feb2004/salk.tdna.shm	009900
TRACK	1	9
SHAPE	ARROW	2
OPTION	TEXTON	1-50
LINK	<font color=009900> SALK T-DNA Homozygous Knockout Line for $4</font> [<a href=/cgi-bin/viewfile?web+a+a+jose+$>seq</a>]
LINK	[<a href=http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12893945>About &amp; Citation</a>]
LINK	[<a href=http://signal.salk.edu/tdna_protocols.html>Vector</a>]
LINK	[<a href=/cgi-bin/tdnainfo?TDNA=$>analysis</a>]
LINK	[<a href=http://www.arabidopsis.org/servlets/SeedSearcher?action=detail&stock_number=$0C target=_blank>Order from ABRC</a>]
LINK	[<a href= http://arabidopsis.info/MultiResult?name=$>Order from NASC</a>]

DATA	TDNA	SALK T-DNA HM (c)	/home/gedb/arab/Feb2004/salk.tdna.rhm	009900
TRACK	1	9
SHAPE	ARROW	2
OPTION	TEXTON	1-50
OPTION	LEGEND	OFF
LINK	<font color=009900> SALK T-DNA Homozygous Knockout Line for $4 by community</font> 
LINK	<br>       [<a href=/cgi-bin/viewfile?web+a+a+jose+$>seq</a>]
LINK	[<a href=http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12893945>About &amp; Citation</a>]
LINK	[<a href=http://signal.salk.edu/tdna_protocols.html>Vector</a>]
LINK	[<a href=/cgi-bin/tdnainfo?TDNA=$>analysis</a>]
LINK	[<a href=http://www.arabidopsis.org/servlets/SeedSearcher?action=detail&stock_number=$5 target=_blank>Order from ABRC</a>]
LINK	[<a href= http://arabidopsis.info/MultiResult?name=$>Order from NASC</a>]

#DATA	TDNA	GABI-Kat FST	/home/gedb/arab/Feb2004/gabi.tdna	999935
DATA	TDNA	GABI-Kat FST	/home/gedb/arab/Feb2004/gabi.tdna.un	999935
TRACK	1	9
SHAPE	ARROW	1
OPTION	TEXTON	1-50
LINK	[<a href=http://signal.salk.edu/cgi-bin/getdnaseq?$>Seq</a>]
LINK	[<a href=http://www.GABI-Kat.de/>GABI-Kat</a>]
LINK	[<a href=http://www.gabi-kat.de/db/showseq.php?term2=$0.5>SimpleSearch</a>]
LINK	[<a href=http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=AJ537513>pAC106</a>]
LINK	[<a href=http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=AJ537514>pAC161</a>]
LINK	[<a href=http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=AY529716>pGABI1</a>]
LINK	[<a href=http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=AY529717>pADIS1</a>]
LINK	[<a href=http://www.gabi-kat.de/db/seed_request.php>Order from GABI-Kat</a>]
LINK	[<a href=http://arabidopsis.info/MultiResult?name="GK-$0.5">Order from NASC</a>]

DATA	TDNA	GABI-Kat Confirmed	/home/gedb/arab/Feb2004/gabi.tdna.cn	999935
TRACK	1	9
SHAPE	ARROW	2
OPTION	TEXTON	1-50
OPTION	LEGEND	OFF
LINK	[<a href=http://signal.salk.edu/cgi-bin/getdnaseq?$>Seq</a>]
LINK	[<a href=http://www.GABI-Kat.de/>GABI-Kat</a>]
LINK	[<a href=http://www.gabi-kat.de/db/showseq.php?term2=$0.5>SimpleSearch</a>]
LINK	[<a href=http://www.gabi-kat.de/db/getseq.php?plantid=$0.5&genecode=$4>Confirmation</a>]
LINK	[<a href=http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=AJ537513>pAC106</a>]
LINK	[<a href=http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=AJ537514>pAC161</a>]
LINK	[<a href=http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=AY529716>pGABI1</a>]
LINK	[<a href=http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=AY529717>pADIS1</a>]
LINK	[<a href=http://www.gabi-kat.de/db/seed_request.php>Order from GABI-Kat</a>]
LINK	[<a href=http://arabidopsis.info/MultiResult?name="GK-$0.5">Order from NASC</a>]

DATA	TDNA	FLAG FST	/home/gedb/arab/Feb2004/flag.tdna	0099FF
TRACK	1	9
SHAPE	ARROW	1
OPTION	TEXTON	1-50
LINK	[<a href=http://signal.salk.edu/cgi-bin/getdnaseq?$>Seq</a>]
LINK	[<a href=http://www-ijpb.versailles.inra.fr/en/sgap/equipes/variabilite/crg/index.htm>About INRA/FLAG FST</a>]
LINK	[<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11752264>FLAGdb</a>]
LINK	[<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12446565&dopt=Abstract>Publication</a>]
LINK	[<a href=http://www-ijpb.versailles.inra.fr/en/sgap/equipes/cyto/ressources/pGKB5.html>pGKB5 Vector</a>]
LINK	[<a href=http://dbsgap.versailles.inra.fr/publiclines/>Order from INRA</a>]

DATA	TDNA	Wisc FST	/home/gedb/arab/Feb2004/wisc.tdna.un	50AA20
TRACK	1	9
SHAPE	ARROW	1
OPTION	TEXTON	1-50
LINK	[<a href=http://signal.salk.edu/cgi-bin/getdnaseq?$>Seq</a>]
LINK	[<a href=http://www.hort.wisc.edu/krysan/2010/default.htm>Wisc</a>]
LINK	[<a href=http://www.hort.wisc.edu/krysan/DS-Lox/>Vector</a>]
LINK	[<a href=http://www.arabidopsis.org/servlets/TairObject?type=germplasm&name=$>Order from ABRC</a>]

DATA	TDNA	Wisc T-DNA HM (c)	/home/gedb/arab/Feb2004/wisc.tdna.rhm	009900
TRACK	1	9
SHAPE	ARROW	2
OPTION	TEXTON	1-50
OPTION	LEGEND	OFF
LINK	<font color=009900> Wisc T-DNA Homozygous Knockout Line for $4 by community</font> 
LINK	<br>       [<a href=http://signal.salk.edu/cgi-bin/getdnaseq?$>Seq</a>]
LINK	[<a href=http://www.hort.wisc.edu/krysan/2010/default.htm>Wisc</a>]
LINK	[<a href=http://www.hort.wisc.edu/krysan/DS-Lox/>Vector</a>]
LINK	[<a href=http://www.arabidopsis.org/servlets/SeedSearcher?action=detail&stock_number=$5 >Order from ABRC</a>]

DATA	TDNA	SAIL FST	/home/gedb/arab/Feb2004/sail.tdna.un	C07829
TRACK	1	9
SHAPE	ARROW	1
OPTION	TEXTON	1-50
LINK	[<a href=http://signal.salk.edu/cgi-bin/getdnaseq?$>Seq</a>]
LINK	[<a href=http://www.tmri.org/en/partnership/sail_collection.aspx>About SAIL</a>]
LINK	[<a href=http://www.arabidopsis.org/servlets/TairObject?type=germplasm&name=$>Order from ABRC</a>]
LINK	[<a href= http://arabidopsis.info/MultiResult?name=$>Order from NASC</a>]

DATA	TDNA	SAIL T-DNA HM (c)	/home/gedb/arab/Feb2004/sail.tdna.rhm	009900
TRACK	1	9
SHAPE	ARROW	2
OPTION	TEXTON	1-50
OPTION	LEGEND	OFF
LINK	<font color=009900> SAIL T-DNA Homozygous Knockout Line for $4 by community</font>
LINK	<br>       [<a href=http://signal.salk.edu/cgi-bin/getdnaseq?$>Seq</a>]
LINK	[<a href=http://www.tmri.org/en/partnership/sail_collection.aspx>About SAIL</a>]
LINK	[<a href=http://www.arabidopsis.org/servlets/SeedSearcher?action=detail&stock_number=$5 >Order from ABRC</a>]
LINK	[<a href= http://arabidopsis.info/MultiResult?name=$>Order from NASC</a>]

DATA	TDNA	RIKEN FST	/home/gedb/arab/Feb2004/ratm.tdna	999999
TRACK	1	9
SHAPE	ARROW	1
OPTION	TEXTON	1-50
LINK	[<a href=http://signal.salk.edu/cgi-bin/getdnaseq?$>Seq</a>]
LINK	[<a href=http://rarge.gsc.riken.go.jp/dsmutant/index.pl>RARGE</a>]
LINK	[<a href=http://www.brc.riken.jp/lab/epd/Eng/catalog/seed.shtml>Order</a>]

DATA	TDNA	JIC SM Line	/home/gedb/arab/Feb2004/sm.tdna.1	00CC99
TRACK	1	9
SHAPE	ARROW	1
OPTION	TEXTON	1-50
LINK	[<a href=http://signal.salk.edu/cgi-bin/getdnaseq?$>Seq</a>]
LINK	[<a href=http://www.jic.bbsrc.ac.uk/science/cdb/exotic/index.htm>JIC SM</a>]
#LINK	[<a href=http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10521516>JIC ATIS</a>]
LINK	[<a href=http://www.arabidopsis.org/servlets/SeedSearcher?action=detail&stock_number=$4,0 target=_blank>Order from ABRC</a>]
LINK	[<a href=http://seeds.nottingham.ac.uk/Nasc/nascsm.lasso?name=$>Order from NASC</a>]
LINK	[<a href=http://www.jicgenomelab.co.uk/docs/mutantdetection/SM.435.pdf>PCR</a>]

DATA	TDNA	CSHL FST	/home/gedb/arab/Feb2004/cshl.tdna	5099CC
TRACK	1	9
SHAPE	ARROW	1
OPTION	TEXTON	1-50
LINK	[<a href=http://signal.salk.edu/cgi-bin/getdnaseq?$>Seq</a>]
LINK	[<a href=http://genetrap.cshl.org>CSHL Ds</a>]
LINK	[<a href=http://genetrap.cshl.org/servlet/TrQuickSearch?GetLine=$0.5&QuickSearch=Get+It>Detail</a>]
LINK	[<a href=mailto:simorows@cshl.edu>Order</a>]

DATA	TDNA	IMA Ds	/home/gedb/arab/Feb2004/imal.tdna	CC5099
TRACK	1	9
SHAPE	ARROW	1
OPTION	TEXTON	1-50
LINK	[<a href=http://signal.salk.edu/cgi-bin/getdnaseq?$>Seq</a>]
LINK	[<a href=http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10590156&dopt=Abstract>about IMA Ds</a>]
LINK	[<a href=http://www.arabidopsis.org/servlets/SeedSearcher?action=detail&stock_number=$4,0 target=_blank>Order from ABRC</a>]
LINK	[<a href=http://seeds.nottingham.ac.uk/Nasc/action.lasso?-token.user=&-response=browse/ima/ima.lasso>Order from NASC</a>]
LINK	[<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?SUBMIT=y&db=nucleotide&term=$>NCBI</a>]

DATA	TDNA	Community FST	/home/gedb/arab/Feb2004/cmts.tdna	CC5099
TRACK	1	9
SHAPE	ARROW	2
OPTION	TEXTON	1-50
OPTION	LEGEND	OFF
LINK	[<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=search&term=$ target=_blank>NCBI</a>] 

DATA	CDNA	GateWay Clone	/home/gedb/arab/Feb2004/salk.gateway.u.2	379937
LINK	 Invitrogen/Salk Gateway clone, originally SSP/Salk pUNI clone.
LINK	[<a href=/pENTR223.doc>pENTR223 Seq</a>]
LINK	[<a href=/pENTR223-map.doc>pENTR223 Map</a>]
LINK	[<a href=/cgi-bin/sspsearch?CLONE=$4>Orignal SSP/SALK U</a>]
LINK	[<a href=http://www.arabidopsis.org/servlet/Search?type=dna&action=search&pageNum=1&search=submit+query&dna_type=clone&order=name&type_1=clone&method_1=2&term_1=$ target=_blank>Order from ABRC</a>]
TRACK	2	5
SHAPE	ARROW	2
OPTION	TEXTON	1-200

DATA	CDNA	SSP cDNA	/home/gedb/arab/Feb2004/salk.ssp.r.2	993720
TRACK	2	4
SHAPE	ARROW	2
OPTION	TEXTON	1-200
LINK	[<a href=/cgi-bin/sspsearch?CLONE=$ target=_blank>SSP</a>]
LINK	[<a href=http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14593172>About &amp; Citation</a>]
LINK	[<a href=/cgi-bin/sspsearch?CLONE=$ target=_blank>Order</a>] - click RAFL

#DATA    CDNA    SSP pUni Clone  /home/gedb/arab/Feb2004/salk.ssp.u.2 663399
DATA	CDNA	SSP pUni Clone	/home/gedb/arab/Feb2004/salk.ssp.u.2	993720
TRACK	2	4
SHAPE	ARROW	2
OPTION	LEGEND	OFF
OPTION	TEXTON	1-200	
LINK	[<a href=/cgi-bin/sspsearch?CLONE=$ target=_blank>SSP</a>]
LINK	[<a href=http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14593172>About &amp; Citation</a>]
LINK	[<a href=http://www.arabidopsis.org/servlets/StockSearcher?action=detail&stock_number=$ target=_blank>Order from ABRC</a>]
#LINK	[<a href=http://godot.ncgr.org/servlets/StockSearcher?action=detail&stock_number=$ target=_blank>Order from ABRC</a>]

DATA	CDNA	Salk cDNA	/home/gedb/arab/Feb2004/salk.slk.s.2	993386
TRACK	2	4
SHAPE	ARROW	2
OPTION	TEXTON	1-200
LINK	[<a href=/cgi-bin/sspsearch?CLONE=$ target=_blank>SALK</a>]
LINK	[<a href=http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14593172>About &amp; Citation</a>]
LINK	[<a href=http://www.arabidopsis.org/servlets/StockSearcher?action=detail&stock_number=$ target=_blank>Order from ABRC</a>]

DATA	CDNA	Salk pUni Clone	/home/gedb/arab/Feb2004/salk.slk.u.2	993386
#DATA    CDNA    Salk pUni Clone /home/gedb/arab/Feb2004/salk.slk.u.2 336699
TRACK	2	4
SHAPE	ARROW	2
OPTION	LEGEND	OFF
OPTION	TEXTON	1-200
LINK	[<a href=/cgi-bin/sspsearch?CLONE=$ target=_blank>SALK</a>]
LINK	[<a href=http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14593172>About &amp; Citation</a>]
LINK	[<a href=http://www.arabidopsis.org/servlets/StockSearcher?action=detail&stock_number=$ target=_blank>Order from ABRC</a>]

DATA	CDNA	TIGR Hypos	/home/gedb/arab/Feb2004/tigr.cdna	339988
TRACK	2	4
SHAPE	ARROW	2
OPTION	TEXTON	1-200
LINK	[<a href=http://www.tigr.org/tdb/hypos/>About TIGR ORFs</a>]
LINK	[<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?SUBMIT=y&db=nucleotide&term=$ target=_blank>GenBank</a>]
#LINK	[<a href=http://www.arabidopsis.org/servlet/Search?type=general&action=search&method=4&name=$ target=_blank>Order from ABRC</a>]

#DATA    CDNA    TIGR ORFs       /home/gedb/arab/Feb2004/tigr.cdna.u  138360
DATA	CDNA	TIGR ORFs	/home/gedb/arab/Feb2004/tigr.cdna.u	339988
TRACK	2	4
SHAPE	ARROW	2
OPTION	LEGEND	OFF
OPTION	TEXTON	1-200
LINK	[<a href=http://www.tigr.org/tdb/hypos/>About TIGR ORFs</a>]
LINK	[<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?SUBMIT=y&db=nucleotide&term=$ target=_blank>GenBank</a>]

DATA	CDNA	RIKEN FL cDNA	/home/gedb/arab/Feb2004/riken.fl.txt	A47949
TRACK	2	4
SHAPE	ARROW	2
OPTION	TEXTON	1-200
LINK	[<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=search&term=$ target=_blank>NCBI</a>]
LINK	[<a href=http://www.brc.riken.go.jp/lab/epd/Eng/index.html target=_blank>Order from RIKEN BRC</a>]

DATA	CDNA	Community cDNA	/home/gedb/arab/Feb2004/salk.atgb.2	398B55
TRACK	2	4
SHAPE	ARROW	2
OPTION	TEXTON	1-200
LINK	[<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?SUBMIT=y&db=nucleotide&term=$ target=_blank>GenBank</a>]
#LINK	[<a href=http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=$&form=6&db=n target=_blank>GenBank</a>]

DATA	CDNA	Community DNA	/home/gedb/arab/Feb2004/salk.atgb.3	398B55
TRACK	2	4
SHAPE	ARROW	2
OPTION	LEGEND	OFF
OPTION	TEXTON	1-200
LINK	[<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?SUBMIT=y&db=nucleotide&term=$ target=_blank>GenBank</a>]

DATA	CDNA	PY TF	//home/gedb/arab/Feb2004/p_y.tf.cdna	9B8B44
TRACK	3	3
SHAPE	ARROW	2
OPTION	TEXTON	1-200
LINK	[<a href=http://signal.salk.edu/cgi-bin/getdnaseq?$>Seq</a>]
LINK	[<a href=http://www.plantphysiol.org/cgi/content/full/135/2/773>About Peking Yale TF</A>]
LINK	[<a href=http://www.arabidopsis.org/servlets/StockSearcher?action=detail&stock_number=$>Order from ABRC</a>]
LINK	(ORF amplified by RT-PCR and cloned into the Gateway( TM) system; 5' and 3' end sequencing has been performed on this clone.)

DATA	CDNA	GSLT cDNA	/home/gedb/arab/Feb2004/gslt.cdna	0799C0
TRACK	3	3
SHAPE	ARROW	2
OPTION	TEXTON	1-200
LINK	[<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?SUBMIT=y&db=nucleotide&term=$ target=_blank>GenBank</a>]
LINK	[<a href=mailto:salanou@genoscope.cns.fr>Order</a>]

DATA	CDNA	RIKEN EST	/home/gedb/arab/Feb2004/salk.rafl.2	593989
TRACK	3	3
SHAPE	ARROW	2
OPTION	TEXTON	1-200
LINK	[<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=search&term=$ target=_blank>NCBI</a>]
LINK	[<a href=http://www.brc.riken.go.jp/lab/epd/Eng/index.html target=_blank>Order from RIKEN BRC</a>]

DATA	CDNA	oRNA EST	/home/gedb/arab/Feb2004/At_oRNA.txt	3959a9
TRACK	3	3
SHAPE	ARROW	2
OPTION	TEXTON	1-200
LINK	[<a href=http://atornadb.bio.uni-potsdam.de/index.php>About Orphan Transcript DB</a>]
LINK	[<a href=http://atornadb.bio.uni-potsdam.de/atornainfo.php?sendform2=yes&identifiers=$ target=_blank>AtoRNA Info</a>]

#DATA	TOME	Salk Tome	/home/gedb/arab/Feb2004/AtTome.txt	005566
DATA	TOME	Salk Tome	/home/gedb/arab/Feb2004/salktome	005566
TRACK	4	8
SHAPE	HISTOGRAM
OPTION	LABEL	L+	AN	FL	RT	SC
OPTION	MIN	50
OPTION	MAX	1000
OPTION	TEXTON	0-0
OPTION	LN	25

#DATA	TOME	NASA Tome	/home/gedb/arab/Feb2004/NASATOME.txt.2	006600
DATA	TOME	NASA Tome	/home/gedb/arab/Feb2004/nasatome	006600
TRACK	5	8
SHAPE	HISTOGRAM
OPTION	LABEL	SC
OPTION	MIN	50
OPTION	MAX	1000
OPTION	TEXTON	0-0
OPTION	LN	36

DATA	EST	ESTs	/home/gedb/arab/Feb2004/EST-2006-12-19.txt	89aa56
LINK	[<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?SUBMIT=y&db=nucleotide&term=$ target=_blank>GenBank</a>]
TRACK	6	4
SHAPE	ARROW	2
OPTION	TEXTON	1-5

DATA	Affy	Affy Probes	/home/gedb/arab/Feb2004/affps.txt	893200
LINK	[<a href=?JOB=EXPR&TYPE=GPL198&QUERY=$ target=_blank>gAtlas</a>]
TRACK	7	2
SHAPE	ARROW	2
OPTION	TEXTON	1-200

DATA	miRNA	ASRP miRNA	/home/gedb/arab/Feb2004/ASRP_miRNA.txt	893267
LINK	[<a href=http://asrp.cgrb.oregonstate.edu/db/microRNAfamily.html>About ASRP miRNA</a>]
LINK	[<a href=http://asrp.cgrb.oregonstate.edu/cgrbfold/index.html?name=At-$>Structure</a>]
TRACK	9	1
SHAPE	TRIANGLE
OPTION	TEXTON	1-200

DATA	miRNA	miRNA Precursor	/home/gedb/arab/Feb2004/miRNA_Precursor.txt	005959
LINK	[<a href=http://sundarlab.ucdavis.edu/mirna/>About miRNA Precursor</a>]
TRACK	9	1
SHAPE	TRIANGLE
OPTION	TEXTON	1-200

DATA	sRNA	ASRP sRNA contig	/home/gedb/arab/Feb2004/ASRP_sRNA.txt2	896723
LINK	[<a href=http://asrp.cgrb.oregonstate.edu/db/>About ASRP sRNA</a>]
TRACK	10	2
SHAPE	TRIANGLE
OPTION	TEXTON	0-0

DATA	sRNA	MPSS sRNA Contig	/home/gedb/arab/Feb2004/mpss.sRNA.17.txt2	5842a0
LINK	[<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16141062&query_hl=3&itool=pubmed_docsum>About MPSS sRNA</a>]
TRACK	10	2
SHAPE	TRIANGLE
OPTION	TEXTON	0-0


DATA	MPSS	MPSS mRNA Target	/home/gedb/arab/Feb2004/mpss.17.ts.txt2	66bb66
LINK	[<a href=http://mpss.udel.edu/at>About MPSS mRNA</a>]
TRACK	8	3
SHAPE	TRIANGLE
OPTION	TEXTON	1-1

DATA	SAGE	SAGE Target	/home/gedb/arab/Feb2004/sage.txt	009933
LINK	[<a href=http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GPL25&view=quick>About SAGE</a>]
TRACK	8	3
SHAPE	TRIANGLE
OPTION	TEXTON	1-1

DATA	USP	AUSP	/home/gedb/arab/Feb2004/ausp.txt	005599
LINK	[<a href=http://peptidome.missouri.edu/>About AUSP</a>]
LINK	[<a href=http://peptidome.missouri.edu/cgi-bin/getprotein.cgi?name=$>Search AUSP</a>]<br>     Note contains sequences of [preproprotein] and [proprotein]
TRACK	8	3
SHAPE	ARROW	2
OPTION	TEXTON	1-5

DATA	BAC	JAtY TAC	/home/gedb/arab/Feb2004/jaty.txt	000099
LINK	[<a href=http://jicgenomelab.co.uk/libraries/arabidopsis/jaty.html>About JAtY</a>]
TRACK	11	3
SHAPE	LINE	3

DATA	EXPR	GPL198 noReps	/home/gedb/arab/Feb2004/GPL198.reps.txt	669988
PLATFORM	GPL198
DATA	EXPR	GPL198 WReps	/home/gedb/arab/Feb2004/GPL198.sngl.txt	668899
PLATFORM	GPL198

Sequence	Arabidopsis thaliana	/home/gedb/arab/Feb2004/AT.fa

Script	No

#Genome	Arabidopsis thaliana	/home/gedb/arab/Feb2004/.CHRSUM	0000AA

#define the HITs, that is a relationship between gene and data
# if gene's direction is 'W'
# //1. tdna pointer to gene (gene's stop + 3UTR > tdna/cdna's start and 
#	gene's start - 5UTR - Promoter > tdna/cdna's stop )
# //2. gene pointer to tdna 
# when the type is TDNA, its stop = start
#HITS	5UTR length	3UTR length	Promoter length
#below are the defaults
HITS	300	300	700
#GIFZIP	/home/gedb/webscript/whirlgif -minimize -trans 0 -o 
##GIFZIP  /home/gedb/webscript/whirlgif -minimize -trans 0 -time 25000 -loop 1 -o