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Transplorer

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Transplorer was developed for BIOBASE GmbH for the prediction of regulatory regions in gene sequences.


Guided Tour >>

 

TRANSPLORERTM is a software package for the recognition and visualization of transcription factor binding sites in DNA sequences.

While TRANSPLORERTM is a pure JavaTM application it can be executed on many platforms.

We have developed the fastest algorithm for matrix based search allowing to quickly process DNA sequences of any length including whole chromosome sequences. TRANSPLORERTM can process DNA sequences in the most popular formats including EMBL, GenBank and FASTA.

TRANSPLORERTM uses the biggest library of matrices derived from TRANSFAC® Professional database and therefore provides a possibility to search for a great variety of different transcription factor binding sites. A search can be made using all matrixes or their subset from the library.

Specific subset of weight matrices along with their cut off similarity values is called "profile". Powerful Profile Editor allows a user to select matrixes from TRANSFAC® Professional or the  user's own matrix libraries. Applying different filters the user can select matrices for transcription factors with specified features: name, taxon, organism, DNA-binding domain and/or tissue specificity. Profile editor also allows a user to specify a cut off similarity value for each matrix providing on fly estimation of a false positive for the given cut off value.

Search results along with search parameters are called project. Powerful Project Wizard guides a user through the analysis steps.

The search results are stored in the database. The results can be presented in tabular form where rows are sites and columns are site features. The user can insert or delete binding sites, comment or change site descriptions. The database also stores experimenta,l structural and regulatory gene regions and extract a EMBL or GeneBank Feature Table.

TRANSPLORER provides a very powerful graphical presentation of the results in the form of a  gene sequence map. There are three map modes: overview mode allows the user to visualize long sequences as a whole; default and detailed modes are used to provide a thorough visualization of results. TRANSPLORER allows a user to use several modes simultaneously: In overview mode the user can select the sequence region of interest and investigate this region more thoroughly in default and/or detailed mode.

A powerful set of filters allows the researcher to visualize binding sites for transcription factors with specified features: name, taxon, organism, DNA-binding domain and/or tissue specificity.

Color schemes are a distinctive feature of TRANSPLORERTM site visualization. Color schemes colorize the site view depending its features: similarity with weight matrix, site type or peculiarities of transcription factor binding with the site. This greatly improves the users comprehension of complicated sequence maps  with many sites.

TRANSPLORERTM is tightly integrated with TRANSFAC® Professional database via its Web interface.


 Free Access to TRANSFAC® Public: Users from non-profit organizations can get free access to TRANSFAC® database through the gene regulation portal: www.gene-regulation.com


[Bioinformatics] [Transplorer] [BioUML] [BioUML Offer] [Gene Studio] [Artemis] [General Finite Element Packages] [PAK-C] [PAK-P] [Biomedical Sciences] [Bioengineering] [Spectra Heap] [Screenshot #2 Tissue and muscle]

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