Manning, Jonathan R, Jefferson, Emily R, Barton, Geoffrey J
Abstract Background Amino acids responsible for structure, core function or specificity may be inferred from multiple protein sequence alignments where a limited set of residue types are tolerated....
Miranda-Saavedra, Diego, Stark, Michael JR, Packer, Jeremy C, Vivares, Christian P, Doerig, Christian, Barton, Geoffrey J
Abstract Background Microsporidia, parasitic fungi-related eukaryotes infecting many cell types in a wide range of animals (including humans), represent a serious health threat in immunocompromised...
Probabilistic prediction and ranking of human protein-protein interactions (2007)
Scott, Michelle S, Barton, Geoffrey J
Abstract Background Although the prediction of protein-protein interactions has been extensively investigated for yeast, few such datasets exist for the far larger proteome in human. Furthermore, it...
Quantification of the variation in percentage identity for protein sequence alignments (2006)
Raghava, GPS, Barton, Geoffrey J
Abstract Background Percentage Identity (PID) is frequently quoted in discussion of sequence alignments since it appears simple and easy to understand. However, although there are several different...
MACSIMS : multiple alignment of complete sequences information management system (2006)
Thompson, Julie D, Muller, Arnaud, Waterhouse, Andrew, Procter, Jim, Barton, Geoffrey J, Plewniak, Frédéric, ...
Abstract Background In the post-genomic era, systems-level studies are being performed that seek to explain complex biological systems by integrating diverse resources from fields such as genomics,...
Jalview: Visualization and Analysis of Molecular Sequences, Alignments, and Structures (2005)
Waterhouse, Andrew, Procter, Jim, Martin, David A, Barton, Geoffrey J
No abstract available.
Martin, David MA, Berriman, Matthew, Barton, Geoffrey J
Abstract Background The function of a novel gene product is typically predicted by transitive assignment of annotation from similar sequences. We describe a novel method, GOtcha, for predicting gene...
James A. Cuff, Ewan Birney, Michele E. Clamp, Geoffrey J. Barton
Motivation: An automatic sequence searching method (ProtEST) is described which constructs multiple protein sequence alignments from protein sequences and translated expressed sequence tags (ESTs)....
Caleb Webber, Geoffrey J. Barton
Motivation: The global alignment of protein sequence pairs is often used in the classification and analysis of full-length sequences. The calculation of a Z-score for the comparison gives a length...
Bioinformatics Applications Note (2004)
Geoffrey J. Barton, Andrew J. Flavell
Summary: An algorithm and software are described that provide a fast method to produce a novel, function-oriented visualization of the results of a sequence database search. Text mining of sequence...
Bioinformatics Applications Note (2004)
Asim S. Siddiqui, Uwe Dengler, Geoffrey J. Barton
Summary: The 3Dee database is a repository of protein structural domains. It stores alternative domain definitions for the same protein, organises domains into sequence and structural hierarchies,...
OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracy (2003)
Raghava, GPS, Searle, Stephen MJ, Audley, Patrick C, Barber, Jonathan D, Barton, Geoffrey J
Abstract Background The alignment of two or more protein sequences provides a powerful guide in the prediction of the protein structure and in identifying key functional residues, however, the...
Protein Sequence Alignment and (2001)
this document. applications to five Ribonucleases, three FAD-binding enzymes and five-cro like DNA binding proteins. The Bacon and Anderson (1986) algorithm shows considerable promise for the...
3Dee: a database of protein structural domains (2001)
Siddiqui, Asim S., Dengler, Uwe, Barton, Geoffrey J.
Summary: The 3Dee database is a repository of protein structural domains. It stores alternative domain definitions for the same protein, organises domains into sequence and structural hierarchies,...
Protein Sequence Alignment and (1998)
Contents 1 Introduction 3 2 Amino acid scoring schemes 3 2.1 Identity scoring : : : : : : : : : : : : : : : : : : : : : : : : : : 3 2.2 Genetic code scoring : : : : : : : : : : : : : : : : : : : : :...
Contents 1 Introduction 3 2 Materials 5 3 Method 5 3.1 General : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : 5 3.1.1 Sequence File : : : : : : : : : : : : : : : : : : : : : : : 7 3.1.2...
User Guide to ALSCRIPT - Sequence alignment to PostScript Version 2.03 (1998)
Contents 1 Update History 1 2 Read This First - VERSION 2.0 2 3 Related Programs 2 4 Availability 2 5 Installing ALSCRIPT 2 6 Brief Description of ALSCRIPT 3 7 New Features in Version 1.4.4 4 8 New...
User Guide to ALSCRIPT - Sequence alignment to PostScript Version 2.0 (1995)
Contents 1 Update History 2 2 Read This First - VERSION 2.0 3 3 Related Programs 3 4 Availability 3 5 Installing ALSCRIPT 4 6 Brief Description of ALSCRIPT 4 7 New Features in Version 1.4.4 5 8 New...
OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracy
Raghava, GPS, Searle, Stephen MJ, Audley, Patrick C, Barber, Jonathan D, Barton, Geoffrey J
Identification of multiple distinct Snf2 subfamilies with conserved structural motifs
Flaus, Andrew, Martin, David M. A., Barton, Geoffrey J., Owen-Hughes, Tom
The Snf2 family of helicase-related proteins includes the catalytic subunits of ATP-dependent chromatin remodelling complexes found in all eukaryotes. These act to regulate the structure and dynamic...
MACSIMS : multiple alignment of complete sequences information management system
Thompson, Julie D, Muller, Arnaud, Waterhouse, Andrew, Procter, Jim, Barton, Geoffrey J, Plewniak, Frédéric, ...
OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracy
Raghava, GPS, Searle, Stephen MJ, Audley, Patrick C, Barber, Jonathan D, Barton, Geoffrey J
Identification of multiple distinct Snf2 subfamilies with conserved structural motifs
Flaus, Andrew, Martin, David M. A., Barton, Geoffrey J., Owen-Hughes, Tom
The Snf2 family of helicase-related proteins includes the catalytic subunits of ATP-dependent chromatin remodelling complexes found in all eukaryotes. These act to regulate the structure and dynamic...
MACSIMS : multiple alignment of complete sequences information management system
Thompson, Julie D, Muller, Arnaud, Waterhouse, Andrew, Procter, Jim, Barton, Geoffrey J, Plewniak, Frédéric, ...
Jefferson, Emily R., Walsh, Thomas P., Roberts, Timothy J., Barton, Geoffrey J.
SNAPPI-DB, a high performance database of Structures, iNterfaces and Alignments of Protein–Protein Interactions, and its associated Java Application Programming Interface (API) is described....
Miranda-Saavedra, Diego, Stark, Michael JR, Packer, Jeremy C, Vivares, Christian P, Doerig, Christian, Barton, Geoffrey J
Sequence alignment for molecular replacement
The problems of gaining accurate protein sequence alignments for molecular replacement are discussed, current techniques explained and strategies suggested.
TarO: a target optimisation system for structural biology
Overton, Ian M., Carter, Lester G., Dawson, Alice, Martin, David M. A., Cameron, Scott, ...
TarO (http://www.compbio.dundee.ac.uk/taro) offers a single point of reference for key bioinformatics analyses relevant to selecting proteins or domains for study by structural biology techniques....
Walsh, Thomas P., Webber, Caleb, Searle, Stephen, Sturrock, Shane S., Barton, Geoffrey J.
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...
The Jpred 3 secondary structure prediction server
Cole, Christian, Barber, Jonathan D., Barton, Geoffrey J.
Jpred (http://www.compbio.dundee.ac.uk/jpred) is a secondary structure prediction server powered by the Jnet algorithm. Jpred performs over 1000 predictions per week for users in more than 50...
Wheeler, Glen L., Miranda-Saavedra, Diego, Barton, Geoffrey J.
The evolution of specific cell signaling and adhesion domains may have played an important role in the transition to a multicellular existence in the metazoans. Genomic analysis indicates that...