Overview of Help-Pages

The main menu of the Genomatix Software Suite is the primary interface to access Genomatix' bioinformatics software packages and databases:

• GePS: Genomatix Pathway System
• LitInspector: Literature and pathway mining.
• MatInspector: The de facto standard for transcription factor binding site search.
• MatBase: Transcription factor knowledge base.
• ElDorado: Extended genome annotation for several genomes (e.g. Homo sapiens, Mus musculus, Rattus norvegicus, Arabidopsis thaliana).
• Gene2Promoter: Retrieve and analyze promoters.
• GEMS Launcher: Genomatix' well known sequence analysis and modeling software package.
• RegionMiner: Analysis of Next Generation Sequencing (NGS) data

• ChipInspector: Starting with version 2.0, Genomatix' microarray analysis software is not present in the main menu anymore but can be downloaded and started as a stand-alone application (download ChipInspector).
• BiblioSphere: Genomatix' gene-gene relation network mining software is no longer available in the main menu, but can be downloaded and started as stand-alone application (download BiblioSphere).

In addition to the software launch buttons the Genomatix Software Suite provides access to all tasks via the navigation bar displayed on top of the main menu. All available tasks are highlighted in yellow, non-available tasks are displayed in gray. The navigation bar is grouped into tasks for

• NGS Analysis / Genomic Region Analysis: RNA expression analysis, ChIPSeq analysis, Region annotation, ...
• Literature & Pathways: GePS and LitInspector
• Genomes & Data: ElDorado, MatBase, ...
• Pattern Search & Analysis: GEMS Launcher tasks for pattern analysis, e.g. MatInspector or ModelInspector
• Pattern Defintion: GEMS Launcher tasks for pattern definition, e.g. MatDefine or FrameWorker
• Alignment & Mapping: GEMS Launcher tasks for sequence alignments, e.g. DiAlign
• Tools: Sequence Tools, BED File Tools, ...
• Projects & Accounts: Provides access to
  • your previously uploaded sequence and BED files and your results from previous analyses
  • the personal page of your account where you can view or change your account data
  • "Password": allows to change the password of your account
  • "Messages": shows messages from Genomatix. We post maintenance notices, software news, etc. here.
  • your personal pattern libraries
• Help: Help for the currently selected program or help overview on all programs

• The "Main menu" link takes you back to the Genomatix Software Suite main menu.
• The "Logout" link releases the current session (for safety reasons or to free a floating account for a colleague).