Products
& Services
BIOBASE - the leading content provider in the field of gene regulation
- offers products and services which allow researchers of the
life-science industry to gain a deeper understanding of all aspects
of gene expression and its regulation. Our databases, analysis
tools and services enable pharmaceutical and biotechnology companies
to effectively and cost-effectively discover and develop drugs.
Our annotation and bioinformatics staff are experts in their respective
fields, and their services are available to customers in need
of expert advice or outsourced analyses.
Databases
The TRANSFAC® System comprising 6 independent databases helps
researchers to understand the transcriptional control of genes,
and the signaling pathways through which control occurs. Functionally
regulated and disregulated conditions are provided in different
databases of this powerful suite of databases. Each of the 6 databases
deals with one special feature in eukaryotic cells. Different
aspects of the situation in the nucleus are described by 4 of
our databases (TRANSFAC®, TRANSCompel®, PathoDB® and
S/MARt DB™) whereas TRANSPATH® describes the signal
transduction from the ligand at the surface of a cell up to the
transcription factor. Cytomer® is a database on cells, organs,
tissues and developmental stages and it is needed to link all
cellular processes to a specific expression profile.
As the basis of the system TRANSFAC® delivers any information
on transcription factors, their genomic binding sites and the
regulated genes. Based on the binding sites matrices which can
be retrieved from multiple site entries in the TRANSFAC® database
analysis tools can be used to elucidate new potential target genes.
Analysis Tools
Match™
Match™ is a powerful tool that integrates into the TRANSFAC®
library of matrix descriptions for transcription factor binding
sites to locate sequence matches.
TRANSFAC´s large library of predefined matrices for transcription
factor binding sites has been tested for accuracy and suitability.
Information about the transcription factors connected to these
matrices can be retrieved from the TRANSFAC® database. Similar
and/ or related matrices have been grouped into matrix families.
Match™ is a search tool for the matrix based identification
of new potential transcription factor binding sites in DNA sequences,
integrated into the TRANSFAC® Professional database.
Patch™
The Patch™ tool is designed for searching potential binding
sites for transcription factors (TF binding sites) in any sequence
which may be of interest. The patterns, which Patch™ uses
for searching, are TF binding sites of the TRANSFAC® Professional
database and the consensus sequences of weight matrices of TRANSFAC®
Professional.
Catch®
Catch® is a tool using the information of TRANSCompel®
to identify potential composite elements in genomic DNA sequences.
TRANSPLORER™
TRANSPLORERTM (TRANScription exPLORER) is a software package
for the identification and analysis of gene regulatory regions.
The current version of TRANSPLORERTM 1.0 includes three powerful
tools for predicting promoter regions and identifying transcription
factor binding sites:
- Dragon Promoter Finder™
- Dragon Gene Start Finder™
- Matrix Search
Services
Gene Regulation Portal
As a special service we have set up a gene regulation portal
which can be accessed on www.gene-regulation.com. Please notice
that usage is free only for non-commercial organisations and that
commercial organisations have to pay for this service.
Consulting
We offer specialized research consulting services in the area
of gene regulation.
We offer complete project coordinations which can reach from
the update of a special area of transcription factors to the complete
utilization of a signal transduction pathway. This could e.g.
comprise the generation of weight matrices from single transcription
factor binding sites and together with our partners we can detect
new potential target genes of these transcription factors. Furthermore
we can model the corresponding signal transduction pathway and
elucidate which cross-reactions should be taken into account when
developing new drugs.
Training
We offer customized training on the use of all our databases
and relevant analysis tools either in-house or at our own facilities.
We will construct a flexible training program that best suits
your needs. Training can range from formal group classroom training
to one-on-one walk-throughs analyzing your research problems.
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