DIALIGN: Multiple DNA and protein sequence alignment at BiBiServ

Nucleic Acids Research

Volumn 32, Issue WEB SERVER ISS., 2004, Pages

  Morgenstern, Burkhard ^a  

^a UNIVERSITY OF GÖTTINGEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

AMINO ACID SEQUENCE; ARTICLE; COMPUTER ANALYSIS; COMPUTER PROGRAM; CONTROLLED STUDY; DNA SEQUENCE; INTERNET; ONLINE ANALYSIS; ONLINE SYSTEM; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

ALGORITHMS; INTERNET; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 3242891684     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh373     Document Type: Article

References (22)

1. Notredame,C. (2002) Recent progress in multiple sequence alignment: a survey. Pharmacogenomics, 3, 131-144.
2. Morgenstern,B., Dress,A. and Werner,T. (1996) Multiple DNA and protein sequence alignment based on segment-to-segment comparison. Proc. Natl Acad. Sci. USA, 93, 12098-12103.
3. Morgenstern,B. (1999) DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics, 15, 211-218.
4. Thompson,J.D., Plewniak,F. and Poch,O. (1999) BAliBASE: a benchmark alignment database for the evaluation of multiple sequence alignment programs. Bioinformatics, 15, 87-88.
5. Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
6. Thompson,J.D., Plewniak,F. and Poch,O. (1999) A comprehensive comparison of protein sequence alignment programs. Nucleic Acids Res., 27, 2682-2690.
7. Notredame,C., Higgins,D. and Heringa,J. (2000) T-COFFEE: a novel algorithm for multiple sequence alignment. J. Mol. Biol., 302, 205-217.
8. Lassmann,T. and Sonnhammer,E.L. (2002) Quality assessment of multiple alignment programs. FEBS Lett., 529, 126-130.
9. Lee,C., Grasso,C. and Sharlow,M.F. (2002) Multiple sequence alignment using partial order graphs. Bioinformatics, 18, 452-464.
10. Abdeddaim,S. (1997) Incremental computation of transitive closure and greedy alignment. Proceedings of the Eigth Annual Symposium on Combinatorial Pattern Matching, Lecture Notes in Computer Science. Vol. 1264, Springer Verlag, Heidelberg, pp. 167-179.
11. Morgenstern,B., Hahn,K., Atchley,W.R. and Dress,A.W.M. (1998) Segment-based scores for pairwise and multiple sequence alignments. In Glasgow,J., Littlejohn,T., Major,F., Lathrop,R., Sankoff,D. and Sensen,C. (eds), Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology, AAAI Press, Menlo Parc, CA, pp. 115-121.
12. Abdeddaim,S. and Morgenstern,B. (2001) Speeding up the DIALIGN multiple alignment program by using the 'greedy alignment of biological sequences library' (GABIOS-LIB). Lecture Notes in Comput. Sci., 2066, 1-11.
13. Morgenstern,B., Rinner,O., Abdeddaim,S., Haase,D., Mayer,K., Dress,A. and Mewes,H.-W. (2002) Exon discovery by genomic sequence alignment. Bioinformatics, 18, 777-787.
14. Brudno,M., Chapman,M., Gottgens,B., Batzoglou,S. and Morgenstern,B. (2003) Fast and sensitive multiple alignment of large genomic sequences. BMC Bioinformatics, 4, 66.
15. Lenhof,H.-P., Morgenstern,B. and Reinert,K. (1999) An exact solution for the segment-to-segment multiple sequence alignment problem. Bioinformatics, 15, 203-210.
16. Sammeth,M., Morgenstern,B. and Stoye,J. (2003) Divide-and-conquer alignment with segment-based constraints. Bioinformatics, 19, ii189-ii195.
17. Devauchelle,C., Grossmann,A., Henaut,A., Holschneider,M., Monnerot,M., Risler,J. and Torresani,B. (2001) Rate matrices for analyzing large families of protein sequences. J. Comput. Biol., 8, 381-399.
18. Morgenstern,B., Goel,S., Sczyrba,A. and Dress,A. (2003) AltAVisT: a WWW server for comparison of alternative multiple sequence alignments. Bioinformatics, 19, 425-426.
19. Miller,W. (2001) Comparison of genomic DNA sequences: solved and unsolved problems. Bioinformatics, 17, 391-397.
20. Chain,P., Kurtz,S., Ohlebusch,E. and Slezak,T. (2003) An applications-focused review of comparative genomics tools: capabilities, limitations, and future challenges. Brief. Bioinform., 4, 105-123.
21. Pollard,D.A., Bergman,C.M., Stoye,J., Celniker,S.E. and Eisen,M.B. (2004) Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics, 5, 6.
22. Brudno,M., Steinkamp,R. and Morgenstern,B. (2004) The CHAOS/DIALIGN WWW server for multiple alignment of genomic sequences. Nucleic Acids Res., 32, W41-W44.