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      SCANPS: a web server for iterative protein sequence database searching by dynamic programing, with display in a hierarchical SCOP browser

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          Abstract

          SCANPS performs iterative profile searching similar to PSI-BLAST but with full dynamic programing on each cycle and on-the-fly estimation of significance. This combination gives good sensitivity and selectivity that outperforms PSI-BLAST in domain-searching benchmarks. Although computationally expensive, SCANPS exploits onchip parallelism (MMX and SSE2 instructions on Intel chips) as well as MPI parallelism to give acceptable turnround times even for large databases. A web server developed to run SCANPS searches is now available at http://www.compbio.dundee.ac.uk/www-scanps. The server interface allows a range of different protein sequence databases to be searched including the SCOP database of protein domains. The server provides the user with regularly updated versions of the main protein sequence databases and is backed up by significant computing resources which ensure that searches are performed rapidly. For SCOP searches, the results may be viewed in a new tree-based representation that reflects the structure of the SCOP hierarchy; this aids the user in placing each hit in the context of its SCOP classification and understanding its relationship to other domains in SCOP.

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          Most cited references17

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          Identification of common molecular subsequences.

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            Amino acid substitution matrices from protein blocks.

            Methods for alignment of protein sequences typically measure similarity by using a substitution matrix with scores for all possible exchanges of one amino acid with another. The most widely used matrices are based on the Dayhoff model of evolutionary rates. Using a different approach, we have derived substitution matrices from about 2000 blocks of aligned sequence segments characterizing more than 500 groups of related proteins. This led to marked improvements in alignments and in searches using queries from each of the groups.
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              Improved tools for biological sequence comparison.

              We have developed three computer programs for comparisons of protein and DNA sequences. They can be used to search sequence data bases, evaluate similarity scores, and identify periodic structures based on local sequence similarity. The FASTA program is a more sensitive derivative of the FASTP program, which can be used to search protein or DNA sequence data bases and can compare a protein sequence to a DNA sequence data base by translating the DNA data base as it is searched. FASTA includes an additional step in the calculation of the initial pairwise similarity score that allows multiple regions of similarity to be joined to increase the score of related sequences. The RDF2 program can be used to evaluate the significance of similarity scores using a shuffling method that preserves local sequence composition. The LFASTA program can display all the regions of local similarity between two sequences with scores greater than a threshold, using the same scoring parameters and a similar alignment algorithm; these local similarities can be displayed as a "graphic matrix" plot or as individual alignments. In addition, these programs have been generalized to allow comparison of DNA or protein sequences based on a variety of alternative scoring matrices.
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                Author and article information

                Journal
                Nucleic Acids Res
                Nucleic Acids Res
                nar
                nar
                Nucleic Acids Research
                Oxford University Press
                0305-1048
                1362-4962
                1 July 2008
                24 May 2008
                24 May 2008
                : 36
                : Web Server issue
                : W25-W29
                Affiliations
                1College of Life Sciences, University of Dundee, Dundee DD1 5EH, 2EMBL-European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, 3Departments of Physiology, Anatomy and Genetics, MRC Functional Genetics Unit, University of Oxford, South Parks Road, Oxford OX1 3QX, 4The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK and 5Biomatters Ltd, Level 6 FAI Building, 220 Queen St, Auckland 1001, New Zealand
                Author notes
                *To whom correspondence should be addressed. +01382 385860+01382 385764 geoff@ 123456compbio.dundee.ac.uk
                Article
                gkn320
                10.1093/nar/gkn320
                2447745
                18503088
                b4f55978-f26b-4ca9-a0b6-ccf66ad56330
                © 2008 The Author(s)

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 31 January 2008
                : 27 April 2008
                : 7 May 2008
                Categories
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                Genetics
                Genetics

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