Q: How to use PAIL server?
A: Firstly, let's go
to the prediction page at http://bdmpail.biocuckoo.org/prediction.php.
Then input FASTA-format protein primary sequence(s) into
the Textbox. You can click on the "Example (human RUNX1
protein)" button for an example sequence. After that,
choose which cut-off value you want and press the "Submit"
button for the final prediction results. Although both
raw sequence and FASTA format are permitted, we recommend
that users employ the FASTA format.
Q: Now I get all the prediction
results that I need, but I can't automatically analyze
them in my own program.
We have provided this functionality for users' convenience!
After you get the prediction results, you may click the
word here in the
sentence "Download the TAB-deliminated data file from
here", and get a TAB-deliminated result file which
should satisfy the need of automatical processing.
Q: There are some "*" characters in predicted peptides. What's their meaning?
PAIL has deployed a window with a length of 13aa (a lysine/K residue flanking with 6aa upstream and 6aa downstream). For lysine residues at N- and C-terminal that can not constitute a full 13aa peptide, PAIL use "*" characters as pseudo amino acids to help the prediction.
4. Q: I have a few questions which are not listed above, how can I contact the authors of PAIL?
A: You may contact Dr.
Yu Xue for details.