Online structural gene annotation tool

Helixer is a tool for structural gene annotations based on a deep-learning approach. In general, the gene annotation of an average genome takes a couple of hours. When a Helixer job finishes, a GFF3-formatted file with the structural annotation data is generated and sent to the specified email address of the user.

Download

For installation of the Helixer application on a local computer, the software and installation requirements are available on GitHub.

Publications

• Holst F, Bolger AM, Kindel F, Günther C, Maß J, Triesch S, Kiel N, Saadat N, Ebenhöh O, Usadel B, Schwacke R, Weber APM, Bolger ME, Denton AK
  Helixer: ab initio prediction of primary eukaryotic gene models combining deep learning and a hidden Markov model.
  Nat Methods. 2025 Nov 24. Online ahead of print.
• Stiehler F, Steinborn M, Scholz S, Dey D, Weber APM, Denton AK
  Helixer: cross-species gene annotation of large eukaryotic genomes using deep learning.
  Bioinformatics. 2020 Dec, 36(22-23): 5291-5298.

The Helixer website is currently undergoing scheduled maintenance. This may result in temporary interruptions. We apologize for any inconvenience and ask for your understanding.

Job submission

• upload a file with nucleotide sequences (one or many records in a valid FASTA format)
  • minimum sequence length of a single record: 25 kbp
  • maximum file size (including all records): 1 GByte
  • optionally, compress the file ('.gz' '.zip' and '.bz2' are supported)
• select the organism lineage 'land plants', 'vertebrates', 'invertebrates' or 'fungi' (required for lineage-specific annotation)
• optionally, provide an email address (where a link to the GFF3-formatted gene annotation results will be sent)
• optionally, specify a label (used as prefix in the GFF3-formatted gene annotation results to specify the source of the nucleotide sequence)