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Genomes and Annotation: ElDorado


[Introduction] [Parameters] [Output]
[Available Genomes] [Source of Elements]

Introduction

ElDorado is the Genomatix genome annotation. It is based on the publicly available reference genome assemblies of 33 different organisms. Information from a variety of different sources together with data generated by Genomatix’ proprietary algorithms is used to set up a database of more than 500 gigabytes of quality checked data. The individual elements are highly linked to external data sources (e.g. NCBI, Ensembl, EntrezGene, ...).

Representing a common sequence basis it allows us to integrate literature based information about gene-gene interactions and pathway annotation from Genomatix Pathway System (GePS) together with experimental gene expression data e.g. from ChipInspector.


ElDorado Content

ElDorado Features


Parameters

ElDorado allows to enter gene names, GeneIDs from EntrezGene, Affymetrix IDs, sequences, or regions on a genomic contig. In case the input is a sequence, this sequence is directly mapped to the genomes.

Organism
Check organism By default the genomes of all organisms listed are searched. Check one or several of the available organisms if you want to restrict your search to individual genomes.
Keyword Search
Enter keywords, accession number, gene name, GeneId, PromoterId or AffyId The gene names included in ElDorado are based on EntrezGene. The input may contain the following gene related keywords:
  • Gene symbols (e.g. HMGA1).
  • Full gene names (e.g. high mobility group AT-hook 1) or more general expressions describing a complex group of genes (e.g. transcription factor or G protein coupled receptor). Wildcards (e.g. COX*) are also possible.
  • GeneIDs from EntrezGene (e.g. 3159).
  • Accession numbers of transcripts that have been mapped to the ElDorado genomes. These include accession numbers from RefSeq (e.g. NM_002131) and Ensembl (e.g. ENST00000327014) as well as full-length transcripts from GenBank (e.g. AK096863).
  • Genomatix Promoter Ids starting with "GXP_" like GXP_311812
  • SNP identifiers from dbSNP (e.g. rs11557697).
  • MicroRNA IDs from miRBase (e.g. mmu-mir-668 or MI0004134).
  • Affymetrix probe set Ids (e.g. 210457_x_at).
    • Only Affymetrix probe set Ids from the default chips of the organisms are searched. You can view and change the default chips on the "Personal" page of your account.
    • The assignment of Affymetrix probe set identifiers to transcripts is based on genomic mapping of each single probe. A transcript will be displayed if at least one single oligo-nucleotide probe of the probe set (usually 11 probes) matches. For mixed probe sets (cross-hybridisation) all relevant transcripts are displayed.

These requests result in a list of genes corresponding to the submitted expression. Each entry consists of a gene description, the gene symbol, and the chromosome it is located on. The request can then be continued by clicking on one of the provided links. In case the element corresponding to the keyword entered is not located nearby a known gene (e.g. rs7510768), only the genomic context is displayed in ElDorado.
or Sequence Input
Choose from your previously uploaded sequences Select a sequence file from the list of your personal sequence files.
or enter the formatted DNA sequence Enter your correctly formatted sequence(s) directly into the form, e.g. with copy and paste.
The following formats are accepted: There should be only IUPAC characters in the sequence, any other characters will be skipped!
or upload a file containing sequence(s) If your browser supports this option, a sequence file can be uploaded.
If you use this option, the file should contain the sequence(s) in either one of the following formats:
or enter accession number(s)

If you're interested in one or several special sequences from a database section, you can supply a list of correct accession numbers in the form. If you want to select more than one accession number, please separate the accession numbers by commas or spaces.

On the Genomatix server accession numbers from the following databases can be entered:

  • GenBank (sections Bacteria, Invertebrates, Other Mammalian, Other Vertebrates, Plants, Primates, Rodents, Viruses, ESTs) (e.g. 'M65229')
  • Eukaryotic Promoter Database (EPD) (e.g. 'EP30014')
  • NCBI Reference Sequences (mRNA sequences) (e.g. 'NM_000402')
  • Genomatix Promoter Database (e.g. 'GXP_107276')
  • dbSNP (e.g. 'rs1234')
or select a region You can also enter a contig ID together with start and end position into ElDorado.
Chip Probes
Display probes from chip Chip probes from fifteen human, mouse, and rat Affymetrix microarrays have been mapped onto the corresponding genomes. The mapped chip probes are displayed in the "Genome Browser", the "Annotation & Analysis" table, and the "Alternative Transcripts" output. Per default the newest chip for each organism is selected.

Output

After the information request is started a report about the ongoing retrieval process is displayed.
For non-ambiguous input data an overview window with all ElDorado results appears:

Result Overview

The ElDorado overview contains links to detailed result pages:

Genomic Context
Genome Browser Graphical representation of the genomic elements found within the sequence with options to zoom in or out.
Annotation & Analysis Table with detailed information for each of the genomic elements found in the sequence and further in-depth analysis.
Detailed Transcript Info Detailed information on the transcripts (transcript quality, genomic location, tissue information, mapping quality, cDNA sequence, protein sequence).
Tissue Profiles Tissue profiles.
SNP Analysis List of annotated SNPs including analysis of their potential functional relevance.
Annotated Sequence Sequence of the genomic fragment in GenBank format. Genomic elements are annotated in the feature table.
Detailed Mapping In case of sequence input, detailed information on the mapping of the sequence including information on splice sites and alignment mismatches.
Gene Oriented Analysis
Alternative Transcripts Overview of the alternative transcripts from a single locus including Affymetrix probe sets that were mapped onto the transcripts.
Comparative Genomics Comparative analysis of transcripts from orthologous loci with promoter annotation.
More Gene Info General gene information from EntrezGene and Gene Ontology as well as Genomatix curated data.
Literature Analysis Literature based information network with citations of closely related genes (table form).