Browsing protein families via the 'Rich Family Description' format

Bioinformatics

Volumn 15, Issue 12, 1999, Pages 1020-1027

  Corpet, Florence ^a   Gouzy, Jérôme ^a   Kahn, Daniel ^a  

^a CEMAGREF   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER INTERFACE; COMPUTER PROGRAM; CONSENSUS SEQUENCE; DATA BASE; INFORMATION RETRIEVAL; INTERNET; PHYLOGENY; PRIORITY JOURNAL; PROTEIN FAMILY; SEQUENCE HOMOLOGY;

EID: 0033493228     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/15.12.1020     Document Type: Article

References (22)

1. Bateman, A., Birney, E., Durbin, R., Eddy, S.R., Finn, R.D. and Sonnhammer, E.L. L. (1999) Pfam 3.1:1313 multiple alignments and profile HMMs match the majority of proteins. Nucleic Acids Res., 27, 260-262. http://www.sanger.ac.uk/Software/Pfam/
2. Boutell, T. (1995) gd 1.2, a graphics library for fast GIF creation, Cold Spring Harbor Labs, http://www.boutell.com/gd/
3. Corpet, F. (1988) Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res., 16, 10881-10890. http://www. toulouse.inra.fr/multalin.html
4. Corpet, F, Gouzy, J. and Kahn, D. (1999) Recent improvements of the ProDom database of protein domain families. Nucleic Acids Res., 27, 263-267. http://www.toulouse.inra.fr/prodom.html
5. Dayhoff, M.O., Schwartz, R.M. and Orcutt, B.C. (1978) In Dayhoff, M.O. (ed.), Atlas of Protein Sequence and Structure Vol. 5, Suppl. 3, National Biomedical Research Foundation, Washington, D.C, pp. 345.
6. Devereux, J., Haeberli, P. and Smithies, O. (1984) A comprehensive set of sequence analysis programs for the vax. Nucleic Acids Res., 12, 387-395.
7. Felsenstein, J. (1993) PHYLIP: Phylogeny Inference Package, Version 3.5, Univ. Of Washington, Seattle, http://evolution.genetics. washington.edu/phylip.html
8. Galtier, N., Gouy, M. and Gautier, C. (1996) SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput. Appl. Biosci., 12, 543-548.
9. Gascuel, O. (1997) BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol. Biol. Evol., 14, 685-695.
10. Henikoff, J.G., Henikoff, S. and Pietrokovski, S. (1999) New features of the Blocks Database servers. Nucleic Acids Res., 27, 226-228. http://www.blocks.fhcrc.org/
11. Higgins, D.G., Thompson, J.D. and Gibson, T.J. (1996) Using CLUSTAL for multiple sequence alignments. Methods Enzymol., 266, 383-402.
12. Hofman, K., Bucher, P., Falquet, L. and Bairoch, A. (1999) The PROSITE database, its status in 1999. Nucleic Acids Res., 27, 215-219, http://www.expasy.ch/prosite/
13. Holm, L. and Sander, C. (1998) Removing near-neighbour redundancy from large protein sequence collections. Bioinformatics, 14, 423-429.
14. Kimura, M. (1983) The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge.
15. Krause, A. and Vingron, M. (1998) A set-theoretic approach to database searching andclustering. Bioinformatics, 14, 430-438. http://www.dkfz-heidelberg.de/tbi/services/cluster/systersform/
16. Livingstone, C.D. and Barton, G.J. (1993) Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation. Comput. Appl. Biosci., 9, 745-756.
17. Parry-Smith, D.J., Payne, A.W., Michie, A.D. and Attwood, T.K. (1998) CINEMA - A novel Colour INteractive Editor for Multiple Alignments. Gene, 221, GC57-63. http://www.biochem.ucl. ac.uk/bsm/dbbrowser/CINEMA2.02/index2.html
18. Schneider, T.D. and Stephens, R.M. (1990) Sequence logos: a new way to display consensus sequences. Nucleic Acids Res., 18, 6097-6100. http://www.bio.cam.ac.uk/cgi-bin/seqlogo/logo.cgi
19. Srinivasarao, G.Y., Yeh, L.L., Marzec, C.R., Orcutt, B.C., Barker, W.C. and Pfeiffer, F. (1999) Database of protein sequence alignments: PIR-ALN. Nucleic Acids Res., 27, 284-285. http://www-nbrf.georgetown.edu/nbrf/getaln.html
20. Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) Improved sensitivity of profile searches through the use of sequence weights and gap excision. Comput. Appl. Biosci., 10, 19-29.
21. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F. and Higgins, D.G. (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res., 25, 4876-4882.
22. Yona, G., Linial, N., Tishby, N. and Linial, M. (1998) A map of the protein space - An automatic hierarchical classification of all protein sequences. Proceedings of ISMB 98 pp. 212-221. http: //www.protomap.cs.huji.ac.iiy