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

Access Information:
Contact the NIH Help Desk: Telephone: 301-496-4357 (open 6:00 am – 6:00 pm).  Email: helpdesk@nih.gov (link sends e-mail), Web: http://support.nih.gov (link is external)
GGA/GMS accounts: (link is external)  Genomatix Genome Analyzer and Genomatix Mining Station:  Contact David Goldstein at goldsted@mail.nih.gov (link sends e-mail) to request an account

Requirements

Access

BTEP classes featuring Genomatix software