Submit your alignment
You have two options to input your sequences in Open-Phylo. Before entering them, we recommend you to pre-align your sequences using a multiple sequence alignment software. Currently, alignments must have a maximum of 350 columns.
You have two options to input your initial multiple sequence alignments:
- Input a file using the FASTA format or MAF format.
- Enter sequences online and input each sequence one-by-one in a text field.
In all cases, you must ensure that all sequences (gaps included) have the same length.
In addition to an initial alignment, Phylo needs a Phylogenetic tree to evaluate the quality of an alignment. Phylogenetic tree are described using the Newick format. A list of supported species is available here. However, you can use identifiers that are not present in this list. The latter are only used to select icons to display in the game.
If you do not have a phylogenetic at hands, we provide a 44 species tree from the UCSC Genome Browser. Currently, this tree is only available with file inputs as it requires an identifier for each sequence (indicated in the header of the files). We are also currently working on implementing a functionality that automatically calculate candidate trees. Meanwhile, you can use PHYLIP or Phylogeny.fr.
Each alignments is assigned to a category. These categories enable us to promote your alignments to Phylo players. Available categories are "Blood and immune system diseases", "Brain and nervous system", "Cancers", "Heart and muscles diseases", "Infectuous disease", "Digestive and respiratory systems diseases", and "Metabolic disorders". If your sequences do not belong to one of these categories, or simply are not related to any disease. You can use the general category (default).
In addition, and when possible, we recommend users to indicate a disease name to their alignment. This information is valuable to players who wish to learn more about the origin of the puzzles they play.
Manage your alignments
Once your alignments uploaded, you will be able to work with them using the data manager. In this page, each row represents one of your alignments. Click on the "View" button to see them.
The viewing mode provides all the information you need to work with your alignments. Your alignments are displayed using the Phylo colored game board. Since alignment can be quite long (up to 350 columns), a sliding frame at the bottom of the page allows you to navigate in your alignment and zoom in different regions. Some regions have been highlighted. They represent the regions that have been selected by Phylo to create puzzles. By default, these puzzles are turned off. You need to confirm their relevance and enable them using the button "Enable level". Once turned on, the gamers will have access to your alignments and will start to play them. Conversely, if you do not like the puzzles, you can simply delete it. If you think that Phylo miss an interesting puzzles (i.e. region poorly aligned) or simply want to dig further your alignment, you can also create new puzzles. To do so, press the "Shift" button and select a region with your mouse. This region will be used to create a new puzzle (N.B.: Puzzles must have 15 to 25 columns).
Move your mouse over a highlighted region (i.e. Phylo puzzle) to see the stats of this puzzle. A frame will appear on your screen and will indicate you how many times this puzzle has been played, what is its highest score as well as its average score. We estimate that 20 to 30 solutions are enough to players to improve (if possible) your alignment. Although, you can collect more solutions if you are not satisfied with the improvement or just wish to study this alignment further.
Building and scoring alignments
On the top-left, a frame indicate the original score of your alignment and the scores obtained by Phylo classic and expert players (classic gamers plays the small alignments while expert improve the full alignment directly). These score are calculated on-demand. To compute them, click on the "Calculate" button. The date of the last evaluation is indicated in this panel.
Phylo allows you to use 3 state-of-the-art scoring functions to estimate the quality of your improvement and the magnitude of the improvement. These functions are Ancestor, MUSCLE, and T-Coffee. In addition, in you do not wish to re-estimate the quality of the submitted alignments with these scoring functions, Phylo offers you to simply use the solution with the highest score in the game (i.e. Phylo score).
You can download your improved alignments anytime by clicking on the "Download" button.
Create your Profile
In order to promote your research, Phylo offers you the possibility to create your own profile in our system. An example of these profile page can be found here. A URL to this profile page will be displayed at the end of each of your puzzles. Therefore, gamers will be able to learn more about your research and eventually (if you wish) to contact you.
This feature is intended to break the wall separating citizen from scientists, engage discussions, and promote genomic research!