Barton,G. J. (1998)
"Protein sequence alignment techniques",
An introduction to common techniques for protein sequence alignment. A PDF and compressed PostScript preprint are also available. I guess this could be in the bookchapters section but since it was refereed, I put it here.
Clamp, M. E., Cuff, J. A. and Barton, G. J. (1998),
"Jalview: Analysis and manipulation of multiple sequence alignments", Embnet News, December 1998 (OX/EBI)
(Note: Links in this article are very out of date and most are dead. See here for information and downloads of the latest Jalview)
Jalview is a multiple sequence alignment editor/viewer and
analysis program written in Java. See here to download the software.
Cuff, J. A., Clamp, M. E. and Barton,G. J. (1998),
"JPred: A consensus secondary structure prediction server", Bioinformatics, 14, 892-893 (OX/EBI)
A PostScript preprint of this paper is available here.
The JPred secondary structure prediction server predicts the
secondary structure of a protein from a multiple sequence alignment of homologous sequences. You can either send a multiple alignment you have created yourself, or a single sequence
and allow the server to generate the alignment for you. Full instructions and documentation are on the server.
Keller, P. A., Henrick, K, McNeil, P., Moodie, S. and Barton, G. J., (1998), "Deposition of Macromolecular Structures",
Acta Cryst. D,54,1105-1108. (EBI)