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An Example for FastM and ModelInspector


[Introduction] [Model Definition] [ModelInspector Output] [References]

Introduction

This example shows step by step how to set up all parameters for FastM and ModelInspector to scan an EMBL section for B1 elements. B1 elements are rodent repetitive sequences that correspond to human Alu sequences.

Characteristic features of B1 elements are:

These features are derived from

Gimbel, W., Schmidt, J., Erfle, V., Werner, T. (1996) A new variant of B1 elements, vB1, identified upstream of a retroviral integration site DNA Sequence 6, 229-232.

Note: The model described here is different from the B1 model contained in the Genomatix genomic repeats library.


Model Element Definition with FastM


Model Overview

Your model "B1_element":
Terminal Iupac Matrix O$TANTMult_repeat

Name Strand Quality
Element 1 TERMINAL REPEAT
length: > 10 bp
matches: > 90 %
Distance Range 10 to 40 bp
Element 2user-defined IUPAC: GTGGTGGCRCAYRCCTTTAATCCCAGCAC+max. 5 mismatches
Distance Range 20 to 40 bp
Element 3Family:
O$TANT
+core sim. > 0.75
optimized matrix sim.
Distance Range 60 to 150 bp
Element 4 MULTIPLE REPEAT
( A )
repetitions: > 12 times
matches: > 75 %
Distance range 20 to 200 bp
last element TERMINAL REPEAT

Start ModelInspector directly with this FastM model.


Sequence Selection for ModelInspector


ModelInspector Output File


References

If you are interested in more details, FastM and ModelInspector are described in