Frequently Asked Questions

Can I upload large genomes?

The current limit for uploaded files is 4000 MB. If you need to annotate input genomes larger than that, it makes sense to run a stand-alone version of Companion on a sufficiently powerful machine, as it hits the limit of this web server. You can find the standalone version of Companion on GitHub. Please follow the instructions there to set up your stand-alone instance.

What species are offered as references?

We import annotated parasite genomes from external sources like VEuPathDB and preprocess them for use as references. Currently, we are offering 434 reference species, which can be seen here.

How many jobs can I run at once?

You can submit as many jobs as you like. They will all be added to the global queue and executed sequentially one after another. This server is a shared resource, so please refrain from submitting many jobs that compute protein-DNA alignments.

What format do the transcript evidence files need to have?

Transcript evidence must be provided in GTF format, for example as produced by Cufflinks (e.g. cufflinks, cuffmerge or cuffcompare). Here is an example:

      Pf3D7_01_v3     Cufflinks       exon    29108   34762   .       +       .       gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; oId "CUFF.2.1"; tss_id "TSS1";
      Pf3D7_01_v3     Cufflinks       exon    35888   37610   .       +       .       gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "2"; oId "CUFF.2.1"; tss_id "TSS1";
      Pf3D7_01_v3     Cufflinks       exon    35202   37610   .       +       .       gene_id "XLOC_000001"; transcript_id "TCONS_00000002"; exon_number "1"; oId "CUFF.2.2"; tss_id "TSS2";
      Pf3D7_01_v3     Cufflinks       exon    38222   39773   .       +       .       gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "1"; oId "CUFF.4.1"; tss_id "TSS3";
      Pf3D7_01_v3     Cufflinks       exon    97430   99013   .       +       .       gene_id "XLOC_000003"; transcript_id "TCONS_00000004"; exon_number "1"; oId "CUFF.9.1"; tss_id "TSS4";
      Pf3D7_01_v3     Cufflinks       exon    99220   104775  .       +       .       gene_id "XLOC_000003"; transcript_id "TCONS_00000004"; exon_number "2"; oId "CUFF.9.1"; tss_id "TSS4";
      Pf3D7_01_v3     Cufflinks       exon    104928  105838  .       +       .       gene_id "XLOC_000003"; transcript_id "TCONS_00000004"; exon_number "3"; oId "CUFF.9.1"; tss_id "TSS4";
      Pf3D7_01_v3     Cufflinks       exon    106191  108971  .       +       .       gene_id "XLOC_000004"; transcript_id "TCONS_00000005"; exon_number "1"; oId "CUFF.10.1"; tss_id "TSS5";
      [...]
    

Please note that the coordinates in this file must match the coordinate system of the corresponding uploaded sequence file and the IDs in the first column must match the sequence headers in the uploaded sequence.

What do I do if I can't find a related species in the reference list, or there is no reference yet?

You need to pick one of the given references to provide models for the gene finders as well as a set of chromosomes for input contiguation. If you can't use any of the references, just disable the contiguation option (which will leave your initial sequence untouched) and pick the closest reference in the list.

We aim to continually extend the list of supported references by importing annotations from databases like EuPathDB. If your reference is annotated and of reasonable size it is quite likely that it will be added in the future.

What software is Companion built on?

The following diagrams illustrate how Companion works and what software components are used:

I have a question but it is not here on this list!

Please send an email to us with your inquiry, we will get back to you shortly.