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FastMis a method to develop user defined models of transcriptional regulatory DNA units (e.g. promoters). Thus, modular organizations of functional sequence regions (e.g. promoters) can be modeled.
Models generated by FastM can then be used with ModelInspector to scan any DNA sequences or sequence databases for matches to the model.
FastM will build a so-called model from the information of
The principles behind FastM and ModelInspector are published in Klingenhoff et al., 1999 (Bioinformatics).
Definition of a Model | |
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Define a new model | You have to enter a name for your model which will be used for
further reference to this model, and select the number of sequence
elements for this model. After you press the "Continue" button, a new form will ask for the type of elements. If you selected the wrong number of elements, you can use your browser's back-button and correct your model. |
Element types | |
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Matrix description |
Select a matrix
or a matrix family from the respective scrollable lists given in
the form. The matrices are taken from the MatInspector matrix library. The matrix names are from all sections of the library and for clarity their names start with one of the following
|
IUPAC string | There are two ways to define a IUPAC
element:
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Transcription start site | The transcription start site (TSS) of genes
can be included as element in promoter models. Including the TSS in promoter
models makes sense when transcription factor binding sites are found in
a conserved distance upstream or downstream of the TSS (like the TATA box).
Transcription factor binding site models generated by FrameWorker can be
extended by including the TSS as additional element.
Important note: Transcription start sites can only be identified in Genomatix promoter sequences, i.e. promoter sequences that have been extracted by Gene2Promoter or the Genomatix promoter databases that are available in GEMS Launcher. For all Genomatix promoter sequences (except the promoters derived from Comparative Genomics) the transcription start site(s) are annotated in the sequence. Searching models including the TSS as element in other sequences will fail because the position of the TSS cannot be found. |
User-defined Model | A model that was previously build (by
FastM or FrameWorker) can be
incorporated into a new model, thus hierarchical models can be build.
Models can be selected from
Parameters:
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Direct repeat | A direct repeat is defined
as a stretch of basepairs that is repeated with a high degree of similarity
in the same sequence.
Parameters:
|
Short multiple repeat |
A short multiple repeat is
defined as a stretch of basepairs that is repeated several times with a
high similarity within the sequence.
Parameters:
|
Hairpin (inverted repeat) |
A hairpin is defined as an inverted
repeat that forms the stem of the hairpin and a stretch of unpaired basepairs
that forms the loop.
Parameters:
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Terminal repeat (only for first element) |
A terminal repeat (direct
or inverted) is defined as a stretch of basepairs that is repeated at the
beginning and at the end of the defined model.
Parameters:
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Distance range definition | |
Select a distance range between two consecutive elements | Please enter the minimum and maximum distance between two elements in
nucleotides.
For determination of the distances the middle positions (so-called
anchor position) of the two consecutive elements are used. |
If you are interested in more details, FastM and ModelInspector are described in
© 2019 Intrexon Bioinformatics Germany GmbH - All rights reserved |