SymPRED help page

Back to SymPRED SYMPRED is a consensus -deriving secondary structure prediction program that uses the PSI-BLAST algorithm to produce input for the individual methods used. The consensus is derived through dynamic programming where all predictions are optimally segmented to a high accuracy level prediction. SYMPRED can be run using any combination of PHDpsi (Rost and Sander, 1993), PROFsec (Rost, unpublished), SSPro2.01 (Pollastri et al, 2002), YASPIN (Lin et al, 2004), JNet (Cuff and Barton, 2000) and PSIPred (Jones, 1999). The SYMPRED server is also part of the global automated assessment server EVA (Koh et al, 2003). Reference: Simossis V.A. and Heringa J. (2004) Optimally segmented consensus secondary structure prediction. Bioinformatics (submitted).

SymPRED is a consensus-deriving algorithm for secondary structure prediction programs. It uses two main consensus-deriving techniques: majority voting and a novel optimally segmenting method that uses dynamic programming. In addition, it employes several weighting strategies for representing the outputs of the secondary structure predictors prior to deriving the consensus predictions. At present, SymPRED can use any combination of six of the top performing secondary structure prediction algorithms, according to the EVA automated assessment server. SymPRED Options: SEQUENCE FORMATS: SymPRED accepts single sequences in the formats dictated by the PSI-BLAST documentation. You can either paste in a sequence in the space provided OR upload a file with your sequence. JOB TITLE: This is also optional. In the case of no entry, the job name will be "Untitled". DATABASES: At the moment we have made NR (non-redundant) and SCOP40 databases available for the PSI-BLAST runs. More Databases will be made available soon. SECONDARY STRUCTURE PREDICTION METHODS: SymPRED can derive a consensus predictions from at least two of the listed secondary structure prediction methods. The default selections were found to yield the best results when tested on the SCOP PDB25 sequence dataset (see reference). CONSENSUS-DERIVING SCHEMES: SymPRED can derive a consensus prediction by either using the simple majority voting method or the novel optimal segmentation method that employs dynamic programming. You have the option to select one of the two, but we advise the use of the default option as it yields more biologically correct results. WEIGHTING SCHEMES: At present, the SymPRED algorithm can weight the predicted secondary structures in five ways: According to a weighted combination of the method-specific average Q3 score over PDB25 and the correlation scores of all pairs of selected methods, According to a weighted combination of the method-specific average SOV score over PDB25 and the correlation scores of all pairs of selected methods, According to the average Q3 score of each method over PDB25, According to the average SOV score of each method over PDB25, According to the correlation scores of all pairs of selected methods. EMAIL: This is a field that you may choose to un-tick if you DO NOT wish to get your results by email. Please note that the results are kept on the server for 15 days max and are erased after that. In order to have a local record of your results you will need to enter the email address you want the results sent to.

Interface written by Victor A. Simossis and Kuang Lin

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