IslandViewer 4 | An integrated interface for computational identification and visualization of genomic islands
Genome Upload

2019/01/11 - MAINTENANCE CONTINUING
Please note that as part of the major move of IslandViewer the custom genome analysis (genome upload) is currently not available but you may still view pre-computed analyses of genomes. If you need any urgent help, please contact us and we apologize for any inconvenience this may cause.

Users can now log in the new user management interface (see LOGIN menu) using Github, Google or Twitter credentials facilitating access to results.

To analyze larger batches of genomes, an HTTP API is available to submit genomes and retrieve results programmatically using curl, python or perl. More information is available here

Genomic island predictions can be calculated for your genome using IslandPick, IslandPath-DIMOB, and SIGI-HMM. More Information. See our FAQs

We only accept user genomes that are formatted in EMBL or GENBANK format. Examples of genome files you should submit: GENBANK, EMBL.

   




Note for incomplete genomes

Incomplete genomes are now accepted as input due to popular demand. However, whole genome analysis is still preferred to reduce false predictions and missing GIs. Please use at your own risk. We suggest to minimize the number of contigs before performing GI analysis and carefully evaluate all results from such custom jobs. Contigs will be ordered against a user-selected reference genome using the Mauve contig orderer (Rissman et al., 2009). Please note that annotation of the contigs is still required.

 

Hints for a successful analysis

Check and see if your genome file contains protein sequences for all CDSs AND the complete nucleotide sequence. A valid genome file should have full protein sequence data (under "\translation" tag within "CDS" primary tag) and nucleotide sequence data under ORIGIN or blank header in GENBANK or EMBL format, respectively. For example:

     CDS   complement(4043..4849)
                ............................
                /translation="MTATFTAIPAEALRLTDLIDAVAERQRKDFGH....
                ............................
ORIGIN
       1 aaacaaacca aatatggatt ttattgtagc .......................

Please refer to the official GenBank documentation for more details.

If you are still having problems, see our FAQs.