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Free online access to human genome retrieval engine - including automated promoter retrieval and comparative analysis

Klaus May may at genomatix.de
Sat Aug 10 05:12:03 EST 2002

The Genomatix Suite – ElDorado, Chip2Promoter, PromoterInspector, and GEMS –
Free online access for academics as well as commercial companies.

More than 100 researchers signed up within the forst three weeks.

Genomatix now offers a complete integrated solution to elucidate the
physical as well as functional context of genes. This can extend into
deciphering gene regulatory networks on a molecular level and provides the
essential genomic background for proteomics approaches.

Subscribers at
will be enabled for
20	ElDorado analyses per month,
5	Chip2Promoter analyses per month with at most 5 accession numbers each,
20 GEMS Launcher analyses per month,
totally free of charge.


Eldorado:	The genome retrieval engine

Basic data resources
-	Complete annotation of the human Genome. More than 50 gigabytes of
condensed, filtered, quality checked and ranked information.
-	A condensation of public available data from a variety of resources
-	PubMed (all abstracts from locus link compiled into “BiblioSphere”)
-	NCBI locus link (50,000 primary transcript structures)
-	SNP databases
-	Gene ontology database (GO)
Proprietary annotation by Genomatix
-	Exclusively available from Eldorado
-	Promoters (20,000 predicted & 10,000 experimentally verified)
-	Quality assessed promoter sequence (gold, silver, bronze)
-	Precompiled promoter structures
-	Transcription factor binding sites (TF binding sites)
-	Promoter modules (cooperating combinations of TF binding sites)
-	Promoter associated SNPs (including SNP/TF evaluation)
-	Scaffold/Matrix Attachment Regions (S/MARs)
-	Single Nucleotide Polymorphisms (SNPs)
Links to other databases
-	Direct links to relevant database entries:
-	PubMed
-	UniGene
-	KEGG, etc:
Multiple organisms (in progress)
-	Coming next:
-	Mouse
-	Arabidopsis
-	Yeast
Philosophy behind ElDorado
-	Single gene focussed physical and functional context analysis.
-	Input by gene name, accession number or raw sequence
-	Lightning fast genome wide cDNA/ EST mapping with splice site analysis
-	Comprehensive representation of compiled results in a single page
-	Interactive graphical representation
-	Innovative interactive 3D graphical representation of complex data
-	Precompiled results by proprietary algorithms:
-	Integration of sequence and literature based  analysis, with cross
-	All selected literature, analyzed for
-	gene/gene co-citations
-	gene/transcription factor co-citations
-	binding site analysis for corresponding promoters/cited TFs
-	List of synonyms, keywords, functional information
ElDorado is flexible and customizable
-	WWW accessible or customized intranet installation.
-	Seamless integration of customer proprietary data.

Chip2Promoter:	Optional HT-promoter retrieval module for ElDorado.

The only way to get hands on quality assessed human promoter sequences for
further analysis, quickly and easily.

Expression array analysis:
-	Logical next step after cluster analysis of gene expression array
-	Automated large scale extraction of human promoters
-	Input from a list of accession numbers or gene IDs.
-	Easy checkbox selection of identified, ranked promoters from list of
-	Can be sorted by molecular function, biological process or cellular
-	Full ElDorado analysis at one click for each promoter and its gene.

Comparative genomics of promoters (in progress)
-	Other Organisms follow as ElDorado grows
-	Automatic selection of orthologous promoters
-	Automatic detection of conserved TF binding sites

>From promoter cluster towards Network
-	Immediate interactive graphical analysis for common TF binding sites
-	Direct submission of selected promoters to GEMS FrameWorker analysis:
-	 common organization of  TF binding sites
-	direct definition of promoter models for database searches

PromoterInspector :	 The first high quality, high throughput promoter
prediction program for mammalian genomes

The gold standard for promoter prediction. Scientifically peer reviewed
breakthrough development (Scherf, M., Klingenhoff, A., Werner, T. (2000).J.
Mol. Biol. 297 (3), 599-606).
-	Works on anonymous sequences (no pre-annotation required)
-	Works on any mammalian genome: mouse, rat, bovine...
-	Fast and lean!  The human genome in one day on a standard workstation
-	Highest available specificity
-	Boost in specificity from 15% to 90%
-	Over 90% true positives
PromoterInspector analysis results for human are accessible from ElDorado.

GEMS: 	Integrated Genome Exploration and Modeling Software
Basic analysis
-	Standard sequence file handling (reverse complement, extract etc.)
-	Finding Restriction enzyme cutting sites
-	Finding transcription factor binding sites (Vertebrates, Plants, Insects,
-	High quality transcription factor weight matrix libraries
-	Individually optimized thresholds for minimum false positives
-	High throughput database searches
-	Oligos, IUPACs, Primer check
-	Retroviral LTRs and primer binding sites
-	Genomic repeats
Genomatix proprietary  analysis
-	Analysis of regulatory DNA regions (e.g. promoters, enhancers)
-	Organizational models of transcriptional regulatory elements (TF-sites)
-	Interactive model definition from experimental data (or literature)
-	Automatic definition of organizational TF-site frameworks in sets of
-	Database scanning with all of the above models
-	Experimental design for site directed mutagenesis of regulatory regions
-	SNP analysis with respect to TF-binding site mutations
-	Automatic determination and validation of  weight matrices from sets of
binding site oligos (SELEX, gel-shifts, footprins, etc.)
-	Comparative analysis of genomic sequences
-	True multiple not Needleman-Wunsch based alignment (DNA and Proteins)
-	High throughput cDNA/EST library mapping
-	DNA signature design
-	Identification of Scaffold/Matrix Attachment regions
Major application areas
-	Chip cluster analysis for molecular basis of co-regulation
-	Phylogenetic analysis of transcriptional regulation (comparative genomics)
-	Pathway-associated co-regulation of gene expression
-	Identification of transcriptional context of genes
-	Identification of transcriptional target genes
Genomatix proprietary databases
-	TF weight matrix library
-	Promoter module database
-	Links to ElDorado
Links to other databases
-	Bucher´s EPD
-	RefSeq
-	Any customer proprietary sequence databases
Philosophy behind GEMS
-	Completely integrated and task oriented
-	Seamless data exchange with ElDorado and Chip2Promoter
-	Easy to use automatic mode or fully adjustable expert mode
-	Modular server/browser based architecture
-	WWW accessible or customized intranet installation
-	Seamless integration of customer proprietary data
-	All libraries extendable by customers or Genomatix services

Klaus J. W. May
Director Sales & Marketing
kmay at genomatix.de
Genomatix Software GmbH
Landsberger Str. 6
D-80339 Munich

Tel.: +49-89-599 766 0
Fax.: +49-89-599 766 55

Genomatix proudly presents:
ElDorado - More than 50 gigabytes of condensed, filtered, quality checked
and ranked information about the human genome. Retrieve or map in seconds!
Chip2Promoter- Automated large scale promoter extraction from a list of
accession numbers or gene IDs.


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