Hosting Genomes Privately on MicrobesOnline

If you have a genome sequence, and wish to analyze it using MicrobesOnline, we can host it for you privately until it is ready for publication. Depending on where we are in our analysis cycle, this process can take up to six months, though we can provide access to our prerelease site so you can view unfinished analyses as they are completed.

At minimum you should have the genome nucleotide sequence reasonably well-assembled (fewer than 100 scaffolds for a bacterial genome is good). We greatly prefer that you also have gene predictions done. Some sequencing centers provide gene models, but not all do--if you do not have gene models, you can use the RAST service (http://rast.nmpdr.org) to generate them for you.

The genome sequence file should be a nucleotide FASTA file with each contig having a unique label. If you are providing gene models, we support a few different formats, including GenBank, EMBL, tab-delimited, and FASTA. If you do not have a GenBank- or EMBL-format file, a tab-delimited or FASTA file must contain at minimum begin, end, strand, and contig name for each gene; the contig name must correspond to the contig names in the genome sequence FASTA file. (You may provide the individual gene sequences or translations, but this is not necessary.) You should also separately provide the name of your genome, and the NCBI taxonomy id if it is available. (If a taxonomy id has not yet been assigned, you should give us whatever information you have about your organism's lineage.)

As an example, see the Desulfovibrio vulgaris DP4 data available at Oak Ridge National Lab. The Gene Model Summary tab-delimited files, together with the FASTA files, are sufficient for us to load into our database. If your sequence is in a different format, please ask, and we will help you in getting the data needed.

Once we have gene models for your genome, we will run them through our analysis pipeline.

If you have not already registered, you should create an account. We will restrict access to your genome to just your MicrobesOnline account. If there are other people you would like to be able to view your genome, you should have them register, and email us with their name(s) and email address(es), so that we can configure them for access. Other users, and the general public, will not be able to see information about your genomes (unless you specify that they can be publicly accessible).

We ask that you cite our paper in the publication of your genome, but you do not need to include us as co-authors for hosting your private data. (You would only need to include co-authors if we contribute additional scientific analyses that are not available from within MicrobesOnline.)

Please contact us at help@microbesonline.org if you wish to coordinate hosting your genome with us. (Please do not send any sequence files to this address; we will contact you with information on where to send sequence files.)

last updated March 2009

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