Genomatix

Major features:
ElDorado/Gene2Promoter/GPD:

• Additional new genomes annotated (now totaling 14 organisms)
  1. Danio rerio (Zebrafish)
  2. Apis mellifera (Honeybee)
  3. Caenorhabditis elegans (Nematode)

• All annotations based on complete proprietary annotation pipeline. No gene predictions. Annotation purely by mapping of more than 530,000 transcripts and >16 million ESTs (EST display/tissue profiling available in the next release after this). Exhaustive cross-mapping with superior proprietary algorithm of all transcripts between the different organisms leading to:

• Superior ortholog grouping in 25,116 homology groups with 3005 groups containing all vertebrates in ElDorado (homo, chimp, rat, mouse, zebrafish, chicken, dog, cow). No paralogs in the groups!
• New ultrafast algorithm for mapping sequences onto genomes
• Precise promoter annotation and prediction by multiple lines of evidence approach
• All single probes from Affymetrix GeneChip probe sets are annotated.

ChipInspector:

• New Affymetrix chips incorporated, including the new Human Exon 1.0 ST array
• Graphical display of identified transcripts and genomic region with single probe positions and significance
• Presence/absence call for experiments without control
• Batch analysis feature for multiple analyses
• Excel/Tab delimited file export of all underlying result data, transcript or single probe based, for further external statistical analysis

BiblioSphere:

• New underlying technology to distinguish homonyms (by “right” and “wrong” context analysis)
• Multi-column data upload
• Range filter for expression values for each column

GEMS Launcher:

• Identification of promoter frameworks with pre-defined mandatory elements in FrameWorker
• Automatic permutation of alternative promoters for FrameWorker
• Extended list comparison with values attached to list elements