What is DAPPLE 2?

DAPPLE 2 represents an alternative method (to machine-learning approaches) to predicting post-translational modification (PTM) sites. It is a pipeline involving BLAST searches (or, for faster results, RAPSearch2 searches) that uses experimentally-determined PTM sites in one organism (or several organisms) to predict PTM sites in an organism of interest. It outputs a table in tab-delimited text format (which can also be easily imported into a spreadsheet program like Excel), which contains various information helpful for choosing PTM 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 predicted orthologues, and so on.

How do I use DAPPLE 2?

As described above, the purpose of DAPPLE 2 is to use experimentally-determined PTM sites in order to predict putative sites in an organism of interest. Thus, there are two main parameters to DAPPLE 2: the organism of interest (the "target organism"), and the database of known PTM sites. The process of selecting these parameters is as follows:

• Target organism

  The target organism is the organism for which you want to predict PTM sites. There are two ways you can select a target organism: by name, or by taxonomic ID. To select an organism by name, click on the "Name" button, and then select your organism from the drop-down box. The organisms are listed alphabetically by scientific name. To select an organism by taxonomic ID, click on the "Taxonomic ID" button. In the text field that appears, type in the taxonomic ID of your desired organism. For example, the taxonomic ID for Sus scrofa (pig) is 9823, so enter 9823 in order to choose pig as our target organism.

• PTM database

  The PTM database is the database containing the experimentally-determined PTM sites that will be used to search the proteome of the target organism. Start by using the first drop-down box to select which PTM you are interested in. Once this is done, the second drop-down box will be filled with the databases that contain data for that PTM. You can either select an individual database, or (for PTMs that are found in more than one database) a non-redundant aggregation of the data from all the databases for that PTM.

• Search method

  You can choose either BLAST or RAPSearch 2 as the search method. BLAST is slower but more sensitive, while RAPSearch 2 is faster but less sensitive. If your target organism is closely related to human (the organism that is generally most well-represented in the PTM databases), we suggest choosing RAPSearch 2; otherwise, we recommend choosing BLAST.

• Maximum number of results to return per known PTM site

  This parameter controls, for each PTM site in the database, the maximum number of matches in the target organism to report. For most applications, we suggest leaving this set to 1, but there may be applications in which this should be increased (e.g., if you are interested in similar PTM sites in paralogous proteins or in different splice variants of the same protein).

Finally, you must enter your e-mail address. Once DAPPLE 2 has finished running, you will receive an e-mail with a link. Click on that link in order to download your results.

If you have any questions or problems, please e-mail us.