For extensive help see: http://www.ibi.vu.nl/programs/pralinewww/ Input parameters are as follows: FASTA: input a set of sequence in FASTA format matrix: substitution matrix matrix options: BLOSUM62 | BLOSUM50 | PAM250 | GON250 | GON120 gapi: gap inititation/open penalty (integer) gapx: gap eXtension penalty (integer) psiit: PSI-BLAST iterations (integer) psipre: PSI-BLAST E-value cutt-off (float) psidb: PSI-BLAST database psidb options: nr | swissprot | pdb | scop10 | scop20 | scop25 | scop35 | scop40 | scop50 | scop70 glpre: score cutt-off for pre-profile global processing (float) iter: number of iterations for pre-profile global processing (integer) alimethod: alignment method alimethod options: psiprepro | prepro | global dssp: DSSP-defined secondary structure search dssp options: noss | dssp sspred: Secondary structure prediction sspred options: noss | psipred | sspro | porter | yaspin tmpred: Transmembrane structure prediction tmpred options: notm | phobius | tmhmm | hmmtop output: output alignment format ouput options: FASTA | MSF email: your email address, if you like to receive an e-mail when the job is finished Successfull completion: completed == true AND status == 1 In case no valid input is provided a ticket with value "0" was returned. All status and statusString values: 1, "Completed"; 0, "Queued/Running"; -1, "Crashed"; -2, "Ticket not found"; -3, "Submission problems: either no valid input or confliction parameters".

WSDL File for Praline. Results can be viewed via the web using this URL: http://zeus.few.vu.nl/jobs/-ticket- getResults returns 0 until results are ready. See http://www.ibi.vu.nl/programs/pralinewww/ for more info.