ConFunc

Structural Bioinformatics Group

Division of Molecular Biosciences
Faculty of Natural Sciences

ConFunc - Conserved residue Function Prediction Server

ConFunc Help Submission Options There are 3 submission options: 1- submit a sequnece and let conFunc do the rest 2- submit a Swiss-Prot accession - conFunc will extract the sequence from Swiss-Prot and make predictions of its function 3- TO BE IMPLEMENTED: submit a multiple sequence alignment containing your chosen query sequence and the other sequences that you would like to used for the prediction process. Note that if you do not provide an accession for the sequence that is to be used then the first sequence in the alignment will be chosen as the query conFunc uses Gene Ontology annotations for Swiss-Prot from the EBI, therefore only sequences in the alignemnt will be used for prediction if they have Swiss-Prot accessions. Further options conFunc has been benchmarked using only PSI-BLAST sequences with e-values less than 1x10-8 and returns upto 2500 sequences from PSI-BLAST. These 2 settings can be modified by changing the values in the relevant text boxes on the conFunc submission page. confidence - Benchmarking was perofrmed using various conFunc threshold settings. You can modify which of these settings is used by changing the confidence value - 1 - highest confidence (best precision, lower recall) - 15 - (lowest precision, highest recall). Job Status Once a query has been submitted the status/results page is displayed. This page displays all the properties of the job and provides an indication of the job's status. This page refreshes every 30 sequences until the job is completed. The current status is displayed which can will be one of the following:
	Status	Description
	submitted	Job submitted not running yet
	running	job started - initial setup running
	running PSI-BLAST	PSI-BLAST being run to identify homologues
	muscle alignment	annotated sequences are being aligned
	generating GO subalignments and e-values	conFunc prediction process
	analysing GO e-value	final conFunc prediction
	finished	Job completed and results displayed below
	error	An error has occured
Results Once completed the status page displays the results. These are split into 2 sections, data that has been generated during the conFunc preidciton process, which includes PSI-BLAST output and MUSCLE sequence alignments. This is followed by the conFunc Function predictions. conFunc Function Predictions conFunc displays 2 lists of GO terms, those that have been predicted by conFunc as functions of the query sequence and those that have been rejected as possible functions of the query. Displayed for each GO term is an e-value and the number of occurences of the term in the set of annotated homologues identified by PSI-BLAST. Further the percentage frequency of each term as a percentage of the total number of annotated homologues identified is display. Each GO has an associated sub-alignment that is used for identifying conserved residues associated with each GO term. These subalignments can be viewed by clicking on the relevant GO term. Please note that some terms have exactly the same e-value, frequency and subalignment, this occurs when the same terms have exactly the same sequences associated with them, this often happens for related terms.

© Structural Bioinformatics Group, Imperial College, London

Mark Wass