Multiple sequence alignment with user-defined constraints at GOBICS

Bioinformatics

Volumn 21, Issue 7, 2005, Pages 1271-1273

  Morgenstern, Burkhard ^a   Werner, Nadine ^a   Prohaska, Sonja J ^b   Steinkamp, Rasmus ^a   Schneider, Isabelle ^a   Subramanian, Amarendran R ^c   Stadler, Peter F ^b   Weyer Menkhoff, Jan ^a  

^a UNIVERSITY OF GÖTTINGEN   (Germany)

^b UNIVERSITY OF LEIPZIG   (Germany)

^c UNIVERSITY OF TÜBINGEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

HOX PROTEIN;

ACCURACY; ARTICLE; AUTOMATION; COMPUTER INTERFACE; COMPUTER PROGRAM; CONTROLLED STUDY; INTERMETHOD COMPARISON; INTERNET; MATHEMATICAL COMPUTING; MOLECULAR EVOLUTION; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN STRUCTURE; SCORING SYSTEM; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

EID: 16344379173     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti142     Document Type: Article

References (14)

1. Brown,D.G. and Hudek,A.K. (2004) New algorithms for multiple DNA sequence alignment. In Jonassen,I. and Kim,J. (eds), Algorithms in Bioinformatics, Vol. 3240 Lecture Notes in Bioinformatics, pp. 314-325.
2. Brudno,M., Chapman,M., Göttgens,B., Batzoglou,S. and Morgenstern,B. (2003) Fast and sensitive multiple alignment of large genomic sequences. BMC Bioinformatics, 4, 66.
3. Lassmann,T. and Sonnhammer,E.L. (2002) Quality assessment of multiple alignment programs. FEBS Lett., 529, 126-130.
4. Morgenstern,B. (1999) DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics, 15, 211-218.
5. Morgenstern,B. (2004) DIALIGN: Multiple DNA and protein sequence alignment at BiBiServ. Nucleic Acids Res., 32, W33-W36.
6. Morgenstern,B., Dress,A. and Werner,J. (1996) Multiple DNA and protein sequence alignment based on segment-to-segment comparison. Proc. Natl Acad. Sci. USA, 93, 12098-12103.
7. Morgenstern,B., Prohaska,S.J., Werner,N., Weyer-Menkhoff,J., Schneider,I., Subramanian,A.R. and Stadler,P.F. (2004) Multiple sequence alignment with user-defined constraints. In Proceedings of GCB'04, Vol. P-53 of Lecture Notes in Informatics, pp. 25-36.
8. Morgenstern,B., Rinner,O., Abdeddaïm,S., Haase,D., Mayer,K., Dress,A. and Mewes,H.-W. (2002) Exon discovery by genomic sequence alignment. Bioinformatics, 18, 777-787.
9. Myers,G., Selznick,S., Zhang,Z. and Miller,W. (1996) Progressive multiple alignment with constraints. J. Comput. Biol., 3, 563-572.
10. Notredame,C. (2002) Recent progress in multiple sequence alignment: a survey. Pharmacogenomics, 3, 131-144.
11. 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.
12. Sammeth,M., Morgenstern,B. and Stoye,J. (2003) Divide-and-conquer alignment with segment-based constraints. Bioinformatics, 19(Suppl. 2), ii189-ii195.
13. Schmollinger,M., Nieselt,K., Kaufmann,M. and Morgenstern,B. (2004) DIALIGN P: fast pair-wise and multiple sequence alignment using parallel processors. BMC Bioinformatics, 5, 128.
14. Simossis,V. and Heringa,J. (2004) Integrating protein secondary structure prediction and multiple sequence alignment. Curr. Protein Pept. Sci., 5, 249-266.