Table 1 of Tasheva, Mol Vis 2004; 10:758-772.

Table 1. Description of the software tools used in this study

The GEMS Launcher software package (release 3.1) was used in this study. GEMS Launcher is an integrated, task-oriented software package which is based on proprietary software tools developed by Genomatix. The set of software tools used to solve the individual tasks and some representative publications [43,92,93] of the basic algorithms are shown.

          Software                   Description
-----------------------------   ----------------------
GEMS Launcher task:             Search for TF binding
MatInspector: To search for     sites described by
transcription factor binding    weight matrices.
sites [43]

GEMS Launcher task:             Search for complex
ModelInspector: To search for   regulatory patterns.
user-defined models [92,93]

GEMS Launcher task:             Search for a common
FrameWorker: For definition     framework of two or
of common framework             more TF binding sites
                                in a set of sequences.

Genomatix Suite:                Retrieve and Analyze
Gene2Promoter                   Promoters

Genomatix Suite:                Extended Genome
ElDorado                        Annotation

Genomatix BibilioSphere         Search for Gene-Gene
                                Gene-TF co-citations
                                in PubMed abstracts

Tasheva, Mol Vis 2004; 10:758-772 <>
©2004 Molecular Vision <>
ISSN 1090-0535