Darwin v. 2.0: An interpreted computer language for the biosciences

Bioinformatics

Volumn 16, Issue 2, 2000, Pages 101-103

  Gonnet, G H ^a   Hallett, M T ^a   Korostensky, C ^a   Bernardin, L ^a  

^a ETH ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER PROGRAM; LANGUAGE; LIBRARY; PRIORITY JOURNAL; SCIENCE;

EID: 0034073452     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/16.2.101     Document Type: Article

References (14)

1. Bairoch, A. and Apweiler, R. (1999) The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999. Nucl. Acids Res., 27, 49-54.
2. Computational Biochemistry Research Group (CBRG) (1999) http: //cbrg.inf.ethz.ch.
3. Gonnet, G.H. and Benner, S.A. (1996) Probabilistic ancestral sequences and Multiple alignments. In Proceedings of Fifth Scandinavian Workshop on Algorithm Theory (1996). Reykjavik, pp. 380-391. LNCS 1097, Springer, Berlin
4. Gonnet, G.H. and Hallett, M.T. (1999) Darwin: A User Manual. Book, available at http://cbrg.inf.ethz.ch.
5. Gonnet, G.H. and Korostensky, C. (2000) Evaluation measures of multiple sequence alignments. J. Comput. Biochem., accepted.
6. Gonnet, G.H., Cohen, M. and Benner, S. (1992) Exhaustive matching of the entire protein sequence database. Science, 256, 1443-1445.
7. Gusfield, D. (1997) Algorithms on Strings, Trees and Sequences. Cambridge University Press, Cambridge.
8. Henikoff, S. and Henikoff, J.G. (1992) Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci1. USA, 89, 915-919.
9. Hillis, D.M. et al. (1996) Molecular Systematics. Sinauer Assoc. Inc, Sunderland, Massachusetts, USA.
10. Knecht, L. (1995) Pairwise alignment with scoring on tuples. In Galil, Z. and Ukkonen, E. (eds), Proceedings of Combinatorial Pattern Matching (CPM '95) Vol. 937, Springer.
11. Korostensky, C. et al. (1998) Identification of proteins in sequence databases using peptides with ragged n- or c-termini generated by sequential endo- and exopeptidase digestions. Electrophoresis, 19, 1933-1940.
12. Korostensky, C. and Gonnet, G.H. (1999) Near optimal multiple sequence alignments using a travelling salesman problem approach. Proc. 6th Annual String Processing and Information Retrieval (SPIRE'99), IEEE Computer Society, September, Cancun, Mexico, pp. 105-114.
13. Saitou, N. and Nei, M. (1987) The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4, 406-425.
14. Stoesser, G. et al. (1999) The EMBL nucleotide sequence database. Nucl. Acids Res., 27, 18-24.