1. Do I need to log in to use Verdant?
You do not need a personal User ID. We have provided a general user ID, but uploaded data and analyses under this ID will be deleted after 72 hours.
2. My upload doesn't seem to be working. What's wrong?
Currently, plastomes must be in a zipped directory, and each plastome must be in its own file. If they are not, then Verdant will not proceed with the upload. You should be seeing an error message if this is the case. If you do not see an error message, either check your e-mail or contact us.
Alternatively, if you have uploaded a sample belonging to an order that is not present in the database, then Verdant will not have references to choose for annotation. We are putting together a set of genes to use in these cases, but the annotations will most likely be questionable.
3. My upload seemed to work, but I am not able to see my data.
There are few possibilities for why you might not see your data.
4. Why is my annotation missing a number of genes?
There are a few possible explanations for this.
5. Why didn’t my search turn up any results?
If you click on “Click Here to Access Your Files” and see only the Parent Directory, there are several possible explanations.
6. Why does it take so long to produce a tree?
Verdant is designed for automated chloroplast annotations and alignment and is not meant to replace a tree-searching program on a cluster. It produces only the RAxML tree for convenience. Because the time required for the analysis scales with the number of plastomes, attempts to produce a tree will take a while. We recommend in these cases that you download the alignment and do a rigorous phylogenetic analysis on another resource such as CIPRES or your institutional server.
7. My search returned sequences files, but some of the taxa are blank. What's going on?
Not all annotated features or regions between features are present in all taxa. Lineages and species with gene loss, such as Cuscuta and other parasitic plants, and analyses including taxa with inversions will create instances where not all taxa share an orthologous segment of the chloroplast genome. In these cases, we have included the missing taxa in the output as blank. This is to inform the user that this region is missing in this taxon. In alignments, these are treated as gaps.
8. My sequence and alignment files have numbers at the beginning of them. What do they mean?
Verdant uses identifying numbers at the beginning of file names to track information about the sequences in the file. Different numbers have different meanings dependent on the type of search implemented.
8. I have found full plastomes in GenBank that are not in the publicly available database in Verdant. Why are they not included?
We use stringent filtering criteria (see McKain et al., supplementary information) to decide which publicly available plastomes to include. These criteria include:
9. Can I use Verdant to make annotations for GenBank submission?
You can download the tbl format annotations and make GenBank submissions using existing for programs for submission (e.g. tbl2asn).
10. Can I delete my plastomes from Verdant?
Yes, you can, but only if you have not made them public yet. To delete an entry, go to the ADD/REMOVE page for a project and proceed to the Select Individual Taxa page. Identify the entry you would like to delete and scroll to the right. You will see the option "DELETE FROM SERVER".
11. My annotations are not correct. Is there something I can do to fix this?
We recommend uploading a trusted annotation for your taxa in this case. If your family is not represented in the VVerdant database or your lineage is highly diverged from its closest relatives in Verdant, the annotation process may not be able to identify identities to gene features. Users can upload annotations directly to Verdant under the Upload Annotations tab.
12. Is it possible that genes exist in my chloroplast genomes that were not annotated?
It is very possible, espeically if the reference chloroplast genomes do not possess genes that are present in your chloroplast genomes. Users can download intergenic regions from their chloroplast genomes using the "Full" keyword in the Search tool. Users can then BLAST these seqeunces to identify possible gene space. Users may also write to Verdant administrators and we can provide unannotated ORFs from chloroplast genomes.