Bioinformatics Web Server

Help

This page explains each input field on the job submission form. Click the Help link next to any field to jump directly to the relevant section below.

Genome FASTA file

Upload the genome sequence of your organism as a multi-FASTA file. Each sequence record must begin with a header line starting with >, followed by the nucleotide sequence. Tiberius predicts genes on all sequences (scaffolds, chromosomes, contigs) present in the file.

Accepted formats

  • .fa.gz or .fasta.gz: gzip-compressed FASTA

Size limit

The maximum accepted upload size is 500 MB.

Requirements

  • Nucleotide sequences only (DNA); protein sequences are not accepted.
  • Sequence names must be unique within the file.
  • Very short contigs (< 1000 bp) are skipped during prediction.

File integrity verification

The job status page shows an MD5 checksum of the genome file exactly as it was received by the server. You can verify that your file was transferred without corruption by comparing this value against the MD5 you compute locally: 

md5sum your_genome.fa.gz

If the two checksums match, the server processed the exact file you uploaded. This is particularly useful when sharing a job link with a collaborator — they can confirm which genome version was used.

Sample data

A small example genome suitable for a test submission is available here:
example_genome.fa.gz (8 scaffolds from the BRAKER example data set; use with the Angiosperms clade model).

Results

Once your job completes, the status page provides download links for the following files:

  • tiberius.gtf.gz — gene predictions in GTF format
  • tiberius.gff3.gz — gene predictions in GFF3 format
  • coding.fasta.gz — predicted coding sequences (CDS) in FASTA format
  • proteins.fasta.gz — predicted protein sequences in FASTA format

All files are gzip-compressed. Decompress them with gunzip before loading them into downstream tools that do not accept compressed input: 

gunzip tiberius.gtf.gz
gunzip tiberius.gff3.gz
gunzip coding.fasta.gz
gunzip proteins.fasta.gz

Many tools (genome browsers, BLAST, BUSCO, etc.) can read .gz files directly — check the documentation of your tool before decompressing.

Clade model

Tiberius uses a deep-learning model trained separately for each taxonomic clade. Select the clade that most closely matches the organism whose genome you are annotating. Using a closely related clade improves gene-structure accuracy.

Clade Suitable for
Mammalia Mammals (human, mouse, cow, bat, etc.).
Vertebrates Non-mammalian vertebrates: fish, amphibians, reptiles, birds.
Insecta Insects (Drosophila, Apis, Tenebrio, etc.). For non-insect arthropods (arachnids, crustaceans, myriapods), the Insecta model may be used as the closest available approximation, but accuracy is not guaranteed.
Angiosperms Flowering plants (Arabidopsis, rice, maize, tomato, etc.).
Fungi Fungi of all major groups (Saccharomyces, Aspergillus, Neurospora, etc.).
Diatoms Diatoms (e.g. Phaeodactylum, Thalassiosira).
Chlorophyta Green algae (Chlamydomonas, Volvox, etc.).

If your organism does not fall clearly into any clade, choose the phylogenetically closest available option. Tiberius does not yet have a universal eukaryotic model.

E-mail address

Provide a valid e-mail address so that we can send you:

  • A confirmation message when your job is accepted and queued.
  • The results (download links) when the job completes successfully.
  • An error notification if the job fails.

Your e-mail address is deleted as soon as the result or error notification has been sent. If sending fails for any reason, it is deleted at the latest after 45 days (when all job files are removed anyway). It is never used for any purpose other than result notification. See the Data Privacy page for full details.

We do not verify e-mail addresses at submission time; please ensure the address is correct, or you will not receive your results.

No personalized human genomic data

By checking this box you confirm that the genome you are uploading is not a personalized human genome sequence — i.e. it does not contain genomic data derived from an identifiable individual.

Reference assemblies (e.g. GRCh38) and non-human genomes are not affected by this restriction. Uploading personalized human genomic data (e.g. a whole-genome sequencing result from a patient or research participant) is prohibited because this service does not provide the safeguards required for the processing of sensitive personal health data under EU GDPR.

Before submitting a job you must confirm that you have read and agree to our Data Privacy Protection Declaration.

The data processed during your job submission are:

  • Your e-mail address: deleted immediately after the result or error notification is sent; at the latest after 45 days.
  • The genome FASTA file you upload: retained for 45 days after job completion, then automatically deleted.
  • The result files produced by Tiberius: retained for 45 days, then automatically deleted.

No data are shared with third parties. The server is operated by the Bioinformatics Group at Universität Greifswald, Germany, and is subject to EU GDPR regulations.