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Jalview Version 2—a multiple sequence alignment editor and analysis workbench
- Andrew M. Waterhouse, J. Procter, David M. A. Martin, M. Clamp, G. Barton
- 16 January 2009
Jalview 2 is a system for interactive WYSIWYG editing, analysis and annotation of multiple sequence alignments that employs web services for sequence alignment, secondary structure prediction and the retrieval of alignments, sequences, annotation and structures from public databases and any DAS 1.53 compliant sequence or annotation server.
The Jalview Java alignment editor
The Jalview Java alignment editor is presented here, which enables fast viewing and editing of large multiple sequence alignments.
The Jpred 3 secondary structure prediction server
The new JPred 3 server includes significant usability improvements that include clearer feedback of the progress or failure of submitted requests and a new software pipeline will enable Jnet/Jpred to continue to be updated in sync with major updates to SCOP and UniProt and so ensures that Jpred 3 will maintain high-accuracy predictions.
Evaluation and improvement of multiple sequence methods for protein secondary structure prediction
Two new sequence datasets are derived which are suitable for cross‐validation of secondary structure prediction methods without artifacts due to internal homology and application of the different published 8‐ to 3‐state reduction methods shows variation of over 3% on apparent prediction accuracy.
JPred4: a protein secondary structure prediction server
JPred4 (http://www.compbio.dundee.ac.uk/jpred4) is the latest version of the popular JPred protein secondary structure prediction server which provides predictions by the JNet algorithm, one of the…
Application of multiple sequence alignment profiles to improve protein secondary structure prediction
The effect of training a neural network secondary structure prediction algorithm with different types of multiple sequence alignment profiles derived from the same sequences, is shown to provide a…
Identification of multiple distinct Snf2 subfamilies with conserved structural motifs
The establishment of a phylogeny for Snf2 proteins provides an opportunity to make informed assignments of function, and the identification of conserved motifs provides a framework for understanding the mechanisms by which these proteins function.
System-Wide Changes to SUMO Modifications in Response to Heat Shock
This comprehensive proteomic analysis of the substrates of a ubiquitin-like modifier (Ubl) identifies a pervasive role for SUMO proteins in the biologic response to hyperthermic stress.
Draft Genome Sequence of the Sexually Transmitted Pathogen Trichomonas vaginalis
The genome sequence of the protist Trichomonas vaginalis predicts previously unknown functions for the hydrogenosome, which support a common evolutionary origin of this unusual organelle with mitochondria.
JPred: a consensus secondary structure prediction server
An interactive protein secondary structure prediction Internet server is presented that simplifies the use of current prediction algorithms and allows conservation patterns important to structure and function to be identified.