Overview of Help-Pages

How to supply DNA sequences
for Genomatix interactive programs

General: Sequence Formats
Accepted DNA sequence formats The following formats for DNA sequences are accepted: There should be only IUPAC characters in the sequence, any other characters will be skipped!
Sequence Input
Choose from your previously uploaded sequences Select a sequence file from the list of your personal sequence files which were saved in the result management in prior analyses (via "add sequences", see below).
Quick Upload Paste your sequence(s) in the form field in one of the accepted formats (see above). Note that sequences pasted in the "quick upload" field are not saved for future use.
Add sequences

Sequences or sequence files uploaded here are automatically saved in the result management for later use:

Enter the formatted DNA sequence(s) Enter your correctly formatted sequence(s) directly into the form, e.g. with copy and paste (see above for accepted formats).
or upload a file containing sequence(s) (max. 100 MB) 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 formats listed above.
Please note, that the size for uploaded files is limited to 100 MB. If you want to analyze larger sequences please contact For whole chromosomes you can use the accession number option below (e.g. 'NC_000001' for human chromosome 1).
Accession number(s) If you are interested in one or several special sequences from a database section, you can supply a list of accession numbers. 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')
Database input
Select one of these database-sections On the Genomatix server the following databases are available:
  • Genomatix Promoter Database: Promoters of annotated genes
    Subset of all human, mouse, and rat promoters. Promoters of
    hypothetical proteins (e.g Loc127262) or genes that are annotated as
    "similar to ..." (e.g. Loc419384) are omitted.
  • Genomatix Promoter Database: Promoters of all genes
    All promoter sequences extracted fromElDoradogenomes with "Genomatix optimized length" (500 bp upstream of the first TSS and 100 bp downstream of the last TSS).
  • Genomatix ElDorado Genomes
    All genomes available inElDorado(human, mouse, rat, chimpanzee, rhesus monkey, dog, opossum, platypus, cow, horse, chicken, zebrafish, fruitfly, Anopheles, honeybee, C. elegans, Arabidopsis and rice)
  • Other databases
    • Philipp Bucher's Eukaryotic Promoter Database (EPD)
    • NCBI Reference Sequences (mRNA sequences)
  • GenBank sections
    The sections Bacteria, Invertebrates, Other Mammalian, Other Vertebrates, Plants, Primates, Rodents, and Viral are available.

In case you have selected a section from the GenBank database you may also restrict the analysis to sequences containing user-defined keywords in their annotation. You can enter keywords which will be searched in

  • the keyword line of the annotation
  • the description line of the annotation
  • the complete annotation

The keyword searches can be combined with "AND" or "OR". Please note that the keywords cannot contain blanks (all blanks will be skipped).

These parameters are hidden by default. You can use the reveal box next to the section header to reveal them!