GeneDB Homepage

GeneDB List Download

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Help
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ID List

Please enter your CDS/RNA systematic IDs either:

Default Organism:
 

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Information Required For Each RNA/CDS

Select fields for Tab-delimited columns, HTML table or FASTA header

Organism Systematic ID Sys. ID (with db prefix)
Primary Name Synonyms Previous Systematic ID
Chromosome Location (coordinates) Product
Orthologues EC Numbers  

Select display options

Column Headers: Yes No Applies to tab-delimited and HTML formats
Separator between columns Applies to tab-delimited (default TAB) and FASTA (default |) formats
Empty columns: Applies to tab-delimited and FASTA formats
Separator within columns: Applies to all formats

Sequence type for FASTA option

DNA (Unspliced sequence of CDS) or sequenced EST
DNA (Spliced sequence)
Intron sequence
Protein sequence
Intergenic Sequence (5' )    Number of bases:
Intergenic Sequence (3' )
CDS/RNA with 5'/3' flanking sequence    5' distance:    3' distance:

Output Format

"Tab"-delimited file HTML Table FASTA Orthologue pasteback

Output destination

Display in the browser window is the default output destination. Users of some browsers (Internet Explorer, Mozilla) have reported problems saving the output to a file. In these cases, the "Save as..." option will force your browser to save the file directly.

Additionally, very large datasets can cause the List Download to fail with a time-out error. The exact number of entries for which a time-out will occur depends upon the requested fields and server load but is typically around 7000. Thus, an option to have download results e-mailed directly, is included.

 Normal page
 Save as...
 Email to
     

 

 

Notes

  1. Location field: For FASTA options the locations will be the genomic coordinates.
  2. Orthologue pasteback: This option returns the List Download form with the input IDs plus the IDs of all orthologues for those IDs.
  3. Orthologues: Orthologue datasets are currently only available for some organisms in GeneDB.
  4. Delimiters: The default column separators are the recommended standard. When changing them, bear in mind (i) that the two should differ and (ii) some chosen download fields may contain the delimiter eg. a product may contain a comma.
  5. Separator within columns: This denotes the character used to separate items in columns which may contain more than one value eg. synonym.

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