Bioinformatics at the OPPF

OPTIC Viewer

The Oxford Protein Target Information Collection (OPTIC) is the main bioinformatics database for storing up-to-date bioinformatics annotations for OPPF targets and serves registered OPPF users. The database management system is SQLServer and not only is OPTIC far faster to use than OPAL (locally licenced versions of software are used), the information is also regularly and automatically refreshed and can generate user alerts. Accession of sequences to the OPTIC database can be trivially scripted and the database has been used for target annotation on the whole-genome scale. The easiest interface to OPTIC is to use OPAL and the SEView applet (see above). An OPPF account is required to use OPTIC.

The OPTIC Viewer is only available to registered users.

RONN Disorder Prediction Tool

The Regional Order Neural Network (RONN) server was developed as a collaboration between the OPPF and Exeter University as a tool for detecting regions of a sequence which are likely to be disordered. Apart from helping to understand potential functional aspects of a protein sequence, this information is also very valuable in construct design since long disordered sequences can adversely affect protein solubility, crystallizability and diffraction quality. In many cases it may even prevent successful structure determination altogether. The RONN server takes a sequence in FASTA format and produces a plot of the predicted probability of disorder for each residue in the sequence. Residues with a disorder probability >50% are predicted to be disordered. The method involves non-gapped sequence alignment between windows along the query sequence and a set of prototype sequences known to be disordered. A neural network is then used to assign a probability of disorder based on the quality of these alignments. RONN has proven itself to be one of the best methods for disorder prediction and is particularly suited to predictions for partially disordered sequences.

The latest version of RONN is publicly available. The software is also freely distributed to academic institutions.

Target Submission

The Target Submission service is the normal way for registered OPPF users to enter new targets in to Oxford Protein Target Information Collection (OPTIC) bioinformatics database. The system preferably takes the DNA and amino-acid sequences in FASTA format and requests information on organism and the names of responsible and executive OPPF users against whom the target should be registered. When the bioinformatics annotation and database entry is complete the responsible user is notified by email. This service is primarily intended for small numbers of targets. For large numbers of targets, such as complete genomes, please contact the OPPF directly.

The Target Submission service is only available to registered users.