Help

DEBT is a web server that predicts both beta-turn location and beta-turn types (I, II, IV, VIII and NS). The theory behind the prediction process was published in *coming soon* and it is highly recommended to read into the background of the methods.

General Tips

DEBT has simple, easy to use interface. However, to benefit most from its use it is strongly recommended to read through this help section. Next to each option on the interface the is a Help small Help link (see to the right) that leads directly to the respective section in this help file.

Job Options

Uploading Files

DEBT can process FASTA files (plain amino acid sequence). PSI-BLAST will be used first to create the PSSM files. Therefore, it will take time to complete the jobs. It is also possible to upload a number of FASTA files at once by combining them in an archive. Currently the following file types can be handled:

Pasting FASTA sequence

It is possible to copy and paste a FASTA sequence. The length of the sequence must al least 15 amino acids. The sequence can only contain the single letter code of the amino acids. The letter X can be used for unknown amino-acids. Numeric characters are NOT accepted. The first line of the pasted sequence can be a title line.

Below is an example of a protein sequence in FASTA format

>1azu
SVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHNWVLST
AADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVFDVSKL
KEGEQYMFFCTFPGHSALMKGTLTL

Job Name

The name of the job is usually made up of the uploaded file name or is given the default file name "sequence" if a FASTA sequence is given. Alternatively, it is possible to define a custom job name, which will be turn up in the name of the output directory sent to the user and the main log filename of the job.

Job Submission

Mail Address

Depending on the number of files submitted, some of the calculations can take from a few minutes to many hours. When a FASTA files are submitted, PSI-BLAST must be used to create the PSSM files which is usually time-consuming. Hence, it is strongly recommended to provide a valid e-mail address where the results can be sent to. However, the e-mail field is not required and the user can simply wait for the calculations to be completed. In this case, an output page appears on the screen (updated every 30 seconds), which displays the status of the submitted job. At the end, a link is provided to download the results.

The output files are all plain text and usually not very large and in general compressed as zip archive.

DISSPred results

DEBT uses DISSPred to predict the secondary structure and the dihedral angles. The output file from DISSPred's prediction can be included in DEBT's output files.

If the compressed folder with the results of the job is bigger than 10 MB (which is very unlikely), a download link is sent via e-mail (if provided) instead of the archive itself. If even e-mails smaller than 10 MB are unwanted or the mail server blocks the DEBT mails, the sending of a download link can be forced with this tickbox. If the user does not wish to provide his e-mail address, the download link will be displayed on the output page as soon as the predictions are finished.

Output File

After the calculations are completed, the output file, together with the log file, are sent by e-mail or can be downloaded. The output file contains the predictions as shown below. The prediction value is "1" if the residue is predicted as beta-turn or beta-turn type and "0" otherwise

image