|
|
Current genome sequencing projects make the complete sequence of the human genome as well as several model organisms publicly available to the scientific community. Thus, the ground is laid for functional sequence analysis of regulatory sequences like promoters on a genomic level. Functional genomics not only requires accurate exon prediction but also demands a thorough analysis of regulatory sequences because important transcription control mechanisms are encoded within these regulatory regions.
Over the past decade nucleotide sequence analysis has focused to a significant extent on protein-coding sequences - often in the form of cDNA. Their corresponding regulatory sequences, especially polymerase II promoters, are located upstream of the coding sequences and are therefore only present in genomic sequences.
The control of gene transcription is a common method used in biological systems to regulate protein expression. Transcriptional regulation in eukaryotes depends upon a series of complex signal transduction networks that ultimately control gene promoter activity via cis acting elements (e.g. enhancers, matrix attachment regions (MARs), locus control regions (LCRs) and trans acting elements (transcription factors).
Gene promoters are essential regulatory structures that regulate the initiation and level of transcription of a gene. Promoters are generally defined as the region of DNA that is located a few hundred basepairs upstream of the site of initiation of transcription. The promoters found in highly regulated genes must be very specific to ensure selective control of transcription. The specificity of the promoter is encoded within its DNA sequence.
Pol II promoters usually consist of multiple binding sites for transcription factors which are necessary for promoter function. However, individual promoter elements require a specific order to constitute a functional promoter. This organization can be dissected into at least three different levels with distinct functionality encoded at each level.
GEMS Launcher has been designed to facilitate solving common tasks in DNA analysis. The tasks are divided into the following groups:
| Pattern Search & Analysis | Search for TF binding sites and complex patterns. Examples are:
|
|---|---|
| Pattern Definition | Definition of TF binding site patterns as weight matrices, definition of complex patterns, and tasks for experimental design. Examples are:
|
| Alignment & Mapping | Examples are:
|
| Genomatix tools | Sequence tools and other tools like comparison of lists. Examples are:
|
| © 1998-2011 Genomatix Software GmbH - All rights reserved |