TRANSPLORERTM is a software package for recognition and
visualization of transcription factor binding sites in DNA sequences. While
TRANSPLORER is a pure JavaTM application it can be executed in
We have developed fastest algorithm for matrix based search letting to process quickly
DNA sequences of any length including whole chromosome sequences. TRANSPLORER
can process DNA sequences in the most popular formats including EMBL,
GenBank and FASTA.
TRANSPLORER 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 user's own matrix libraries.
Applying different filters user can select matrices for transcription factors
features: name, taxon, organism, DNA-binding domain and/or tissue specificity.
Profile editor also allows a user to specify cut off similarity value for each
matrix providing on fly estimation of false positive for the given cut off
Search results along with search parameters are called project. Powerful
Project Wizard guide a user trough 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. User can
insert or delete binding sites as well as make comments or change site
descriptions. The database also stores experimental structural and regulatory
gene regions extract EMBL or GeneBank Feature Table.
TRANSPLORER provides a most powerful graphic presentation of results
in the form of gene sequence map. There are three map modes: overview mode
allows user to visualize long sequences as a whole, default and detailed
modes are used to provide thorough visualization of results. TRANSPLORER
allows a user to use several modes simultaneously: in overview mode user can select the
sequence region of interest and investigate this region more thoroughly in
default and/or detailed mode.
Powerful set of filters allows the researcher to visualize binding sites for
transcription factors with the specified features: name, taxon, organism,
DNA-binding domain and/or tissue specificity.
Color schemes are distinctive feature of TRANSPLORER site visualization.
Color schemes colorize site view depending its features: similarity
with weight matrix, site type or peculiarities of transcription factor binding
with the site. This improves greatly user comprehension of complicated
sequence map with a lot of sites.
TRANSPLORER is tightly integrated with
TRANSFAC® Professional database
via its Web interface.