DAPPLE represents an alternative method (to machine-learning approaches) to predicting phosphorylation sites in an organism of interest. It is a pipeline involving BLAST searches that uses experimentally-determined phosphorylation sites in one organism (or several organisms) to predict phosphorylation sites in an organism of interest. It outputs a table in tab-deliminated text format (which can also be easily imported into a spreadsheet program like Excel), which contains various information helpful for choosing phosphorylation sites that are of interest to you, such as the number of sequence differences between the query site and the hit site, the location of the query site and the hit site in their respective intact proteins, whether the corresponding intact proteins are reciprocal BLAST hits (and thus predicted orthologues), and so on.

The following is a web interface to DAPPLE. If you would instead like to run DAPPLE on your own machine, you may download it here. This .zip file includes instructions for setting up DAPPLE.

Creative Commons LicenseDAPPLE is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. If you would like to use it for commercial purposes, please contact us.

Step #1: Target organism

Please select the target organism (for which you want to predict phosphorylation sites) from the list below.

Alternatively, choose a proteome file (multi-FASTA format) from your local computer to upload. Ensure that the file name contains no spaces or special characters, and that the proteome file contains no blank lines.

Step #2: Known phosphorylation site data

Please select the dataset of known phosphorylation sites that you would like to use. You may choose from four different databases:
  • PhosphoSitePlus (Contains phosphorylation sites from a variety of organisms, mostly mammals)
  • phospho.ELM (Contains phosphorylation sites from a variety of organisms)
  • P3DB (Contains phosphorylation sites from plants)
  • PhosphoGRID (Contains phosphorylation sites from Saccharomyces cerevisisae only)

We would like to thank the developers of these databases for kindly giving their permission to use their data with DAPPLE.

Alternatively, choose a file from your local computer to upload. Click here to view a sample of the required format.

Note: As some of these databases are quite large, DAPPLE can take a significant amount of time to run (more than a day for PhosphoSitePlus). Please run only one instance of DAPPLE at a time. If you wish, you may also use the standalone version of DAPPLE, for which you can run as many simultaneous instances as you like (or your machines will allow).

Step #3: Max results per query

Please select the maximum number of results to return per known phosphorylation site.

Step #4: E-mail address

Please enter your e-mail address here. Once your job is finished running, you will receive an e-mail with a link where you can download the results.

Step #5: Submit!

Image credit: Flickr user Soggydan.