Overview of Help-Pages

Annotation & Analysis

Introduction

The ElDorado Annotation & Analysis page provides a table with the annotation of all functional elements within the mapped genomic sequence.
Additionally, a number of interactive tasks as well as links to more detailed relevant information for specific elements is shown.

For a detailed description of the annotated elements please see this page.

• All functional elements are sequentially ordered by their start positions on the genomic sequence fragment.
• For single nucleotide polymorphisms (SNPs) a direct link to functional SNP analysis by Genomatix is provided.
• microRNAs are given by their genomic location only. For further annotation a link to miRBase (Sanger Institute) is provided.
• Promoter regions can be analyzed for potential transcription factor binding sites using the analyze link in the annotation table.
• For conserved regions a direct link to the corresponding region in the other organism is provided.
• The DNA sequence of each individual element can be extracted using the check box in the extraction column of the annotation table and the extract sequences option at the bottom of the table.
• For clarity, especially in case of a long result list of elements, the page starts with a selection table for including or excluding particular elements in the annotation table. Elements with many matches like modules or SNPs are excluded by default.

Sections

The ElDorado Annotation & Analysis page contains the following sections:

• Interactively include/exclude elements listed in the annotation table
• The annotation table
• The extract sequences option

Interactively include/exclude elements listed in the annotation table

• By default, the Promoters, Transcription Start Regions, and Primary Transcripts found in the genomic sequence are listed in the annotation table. Other elements are excluded; to see them select the corresponding check boxes and click on Re-Display Page.
• The total number of elements for each element type found is given in parenthesis.

Example:

The annotation table

The annotation table lists the elements mapped to the sequence fragment of your request. The elements annotated on the (+) strand and the elements annotated on the (-) strand are shown in two separate tables.

• The elements are ordered relative to their start positions (see column Start) in the genomic sequence fragment.
• Description of the table columns:
  
  • Type of Element: describes the class the element belongs to. Genomatix annotated elements are printed in bold.
  • Start and End: start and end positions of the elements on the genomic contig.
  • Strand: strand orientation of the elements. Possible values: +, -, ±, n/a (not available).
  • Length: length of the element in base pairs.
  • Name: shows the name of the element, e.g. the Genomatix Locus or transcript ID, or the name of a Genomatix model.
  • Annotation / Analysis:
    • Shows further annotation and information for most elements (e.g. gene description).
    • Promoter regions can be further analyzed regarding potential transcription factor binding sites using the "Analyze for binding sites" link provided.
    • For variations, i.e. Single Nucleotide Polymorphisms (SNPs) a link to the Genomatix' tool for functional SNP analyses is provided.
    • For primary transcripts, links to detailed gene information, and comparative genomics (if applicable) are available.
    • For Affymetrix probes, the x- and y-coordinates of the corresponding probe on the chip are given in parentheses.
  • Extraction:
    • The underlying sequence of an element can be extracted by selecting the relevant check box and using the extract sequences option.
• By default, all transcripts annotated in the genomic region are displayed. Individual transcripts can be deselected by unchecking the transcript and pressing the button Re-Display Page.

Example (G6PD):

The extraction options

Extract DNA sequences / genomic regions of elements listed in the annotation table.

• You can extract:
  • elements selected by check boxes in the annotation table (the button "Check all matches" below the annotation table allows to select all elements)
  • elements plus/minus a user-defined number of base pairs upstream and downstream of each element
• Elements can either be extracted as sequence file or as BED file.
• Elements located on the '-' strand are extracted as reverse complement.

Example: