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