Genomes and Annotation: ElDorado

[Available Genomes] [Source of Elements]

Introduction

ElDorado is the Genomatix genome annotation. It is based on the publicly available reference genome assemblies of 26 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 gigabyte 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.

ElDorado Content

Transcripts with exon/intron structure, UTRs, CDS, and protein sequence
Promoters for each transcript analysed for transcription factor binding sites and regulatory modules
CAGE tags, providing additional experimental support for full length transcripts
PromoterInspector predictions
microRNAs
SNPs and their effects on transcription factor binding sites and protein sequences
genomic repeats
SMARs
genomic location for individual probes from Affymetrix chips

ElDorado Features

The gene name query of ElDorado supports extended lists of gene name synonyms and variants.
Very fast algorithm for exon mapping evaluating the cDNA for canonical splice sites
Detailed gene information, integrating information from different public sources (e.g. EntrezGene, GeneOntology) with manually curated gene-gene interactions by Genomatix.
Comparative Genomics allows you to compare the annotation available for a group of orthologous genes and to identify corresponding promoter regions for the analysis of phylogenetically conserved promoter elements.
Literature analysis gives you access to the genes cocited in the scientific literature providing direct links to Genomatix Pathway System (GePS) for further in-depth analysis.

Parameters

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

Keyword Search
Enter keywords, gene name, accession number, 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) and Ensembl (e.g. ENSG00000137309). 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. Per default, all ElDorado database tables containing gene related keywords are searched in a defined order. To restrict your search to a certain keyword (e.g. Gene IDs or gene symbols), choose it from the list to the right of the text field. 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 for mapping (minimum length: 15 bp)
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: plain sequence format EMBL FASTA GCG, RSF (several sequences) GenBank IG 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: plain sequence format EMBL FASTA GCG, RSF (several sequences) GenBank IG
or enter an accession number	If you are interested in a special sequence from a database section, you can supply a correct accession number in the form. 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 Region Input
or select a region	You can also enter a genomic region with its contig or chromosome ID (e.g. NC_000001 or chr1) together with either a genomic start and end position (9500000 - 1000000) or a band id (e.g. p35.3 or q41) Note that the species / genome can be selected via the "Current Genome" option (top right of page).
Select genome(s) to search
Select organism(s)	By default the genome of the currently selected genome (top right on the page) is searched. Check one or several of the other available organisms if you want to extend your search to other genomes.

Chip Probes
Display probes from chip	Chip probes from several 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).