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Contact: michele@ebi.ac.uk |
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We have developed techniques for single sequence database searching, multiple sequence alignment and pattern scanning. Current work centres on the SCANPS database searching program that allows a protein or DNA query to be compared to a database by rigorous dynamic programming algorithm. A server for SCANPS is available here.
Contact: geoff@ebi.ac.uk |
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Good training and test data sets are essential when developing sequence comparison algorithms. The OxBench project has developed rigorous datasets and software to evaluate the comparative accuracy of techniques for:
(a) multiple protein sequence alignment,
(b) 3D structural database searching,
(c) protein sequence database searching,
(d) protein fold recognition.
A server specific to the OxBench project will be accessible here.
Contact: geoff@ebi.ac.uk
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A long-term interest of the group is protein secondary structure prediction. Work on blind prediction of secondary structure for Annexins, SH2 domains and other protein domains has led to current research in analysis of prediction methods.
The JPred secondary structure prediction server is one product of this research.
Contact: james@ebi.ac.uk |
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Fold recognition aims to extend the detection of homology further than is possible with pure sequence comparison methods. Work is in progress to extend the capabilities of the MAP algorithm for protein fold recognition.
Contact: geoff@ebi.ac.uk or james@ebi.ac.uk |
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Early semi-automatic methods such as AMAS for analysis of multiple sequence alignments lack a fast interactive response. The JalView editor written in Java forms the core of new developments to analyse multiple alignments.
Contact: michele@ebi.ac.uk |
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The Common Object Request Broker Architecture provides a mechanism to communicate objects on a network. EBI has an initiative to support access to its databases through CORBA. A demonstration of CORBA applied to the Pfam multiple sequence alignment database is available here.
Contact: michele@ebi.ac.uk |
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