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External Services News from the EBI Rodrigo Lopez, Rob Harper, and Peter Stoehr. EBI's commitment to provide services to external users continues to push the limits of our hardware infrastructure. The recent acquisitions of more computers from SGI (4 x 4 CPU Origin 200's and 2 x 16 CPU Origin 2000īs) will provide a wider window into these services and allow for faster and more reliable delivery of results. Interactive users, which account for 80% of all job submissions, will benefit the most from this upgrade while bulk e-mail users should see much better response times. Users of SRS will also see a major boost in performance once a dedicated 4 x R12K Origin 200 is on-line. This machine is a dedicated server to SRS and as such will provide much better performance to our 35,000+ users per day and obviously allow room for many more. The new setup will provide enhanced availability using multiple redundant hosts and we hope full off-line indexing which should result in no downtime at all. Currently SRS5.x and SRS6.x (under development) are available from the EBI. EBI continues to strive to tighten collaborations with the authors of Fasta, WU-Blast and Clustalw, Dr. Bill Pearson for the University of Virginia, Dr. Warren Gish from Washington University and Dr. Toby Gibson, et al. from EMBL in Heidelberg, respectively. The latest news regarding fasta3 at the EBI is the addition of all programs in the package to our external service. Of particular importance are fasts3 and fastf3 which, respectively, compare linked and mixed peptides to a protein databank. Fastx, fasty, tfastx and tfasty are now also available. For more details please refer to our fasta3 service. The EBI maintains a mirror for the distribution of the fasta package. WU-Blast 2.0 continues to grow in popularity. The implementation and addition of more filters has improved the results and the speed of the searches considerably: dust, seg, pseg, xnu and seg+xnu. Better memory handling and masked sequence (filtered) processing have been implemented thus providing better reliability and performance. More details can be found at our blast service. Fasta and blast have a result viewer called Mview, developed by Dr. Nigel Brown at the EBI, which has proved very popular with our users. The user may access this viewer only in interactive mode after the results of a search are displayed. To compliment this viewer and to show off some of niceties in sensitivity which fasta3 offers we are currently developing and testing a simple graphical display. This one can be accessed from within the same results page and provides an overview of search with colour tags indicating Smith-Waterman scores as well as Expectation values. We believe this view simplifies and improves considerably the interpretation of fasta's results and quite a few surprises have emerged from using it! The parallelised version of clustalw in use at the EBI has emerged from work carried out by Haruna Cofer at SGI's Applications Development Dept. in the US. This version of clustalw has proven to be so fast and efficient that the usage statistics for this application have surpassed demand for usage of fasta3! As an external service, clustalw is only available in interactive mode but we are considering the addition of an e-mail interface in order to allow bulk submissions. Once again, more details can be found at the clustalw service. The top page of the http://www2.ebi.ac.uk/ server, also called the 'tools server', is an important one to follow up. In this page, the user will find all the official external services as well as new developments which are being introduced as a service at the EBI. Some recent examples of these include the Mutation checker (locate mutations in DNA sequences), Jpred (A consensus method for protein secondary structure prediction) and Strudl (Identification of protein domains from atomic coordinates). Article by: Rodrigo Lopez et al. Resources and further information
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Direct questions or comments to Bioinformer Editor. This page last modified Wednesday, 11 August, 1999. (c) 1997-1999 EMBL-EBI. All Rights Reserved. |