Manipulating multiple sequence alignments via MaM and WebMaM

Nucleic Acids Research

Volumn 33, Issue SUPPL. 2, 2005, Pages

  Alkan, Can ^a   Tüzün, Eray ^b   Buard, Jerome ^c   Lethiec, Franck ^d   Eichler, Evan E ^b   Bailey, Jeffrey A ^e   Sahinalp, S Cenk ^f  

^a CASE WESTERN RESERVE UNIVERSITY   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

^c INSTITUTE OF HUMAN GENETICS   (France)

^d LIRMM   (France)

^e CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^f SIMON FRASER UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER GRAPHICS; DATA ANALYSIS SOFTWARE; DNA DETERMINATION; EXON; GENE SEQUENCE; GENETIC DATABASE; GENETIC VARIABILITY; INFORMATION PROCESSING; INTERNET; NUCLEOTIDE REPEAT; PHYLOGENY; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; COMPUTER ANALYSIS; COMPUTER INTERFACE; COMPUTER PROGRAM; CONTROLLED STUDY; DNA SEQUENCE; GENETIC CODE; GENOMICS; MOLECULAR PHYLOGENY; PROCESS OPTIMIZATION; SEQUENCE DATABASE; METHODOLOGY;

GENOMIC DNA;

EXONS; GENOMICS; INTERNET; PHYLOGENY; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 23144459797     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki406     Document Type: Article

References (9)

1. Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
2. Lipman,D.J., Altschul,S.F. and Kececioglu,J.D. (1989) A tool for multiple sequence alignment. Proc. Natl Acad. Sci. USA, 88, 4412-415.
3. Eddy,S.R. (1998) Profile hidden Markov models. Bioinformatics, 14, 755-763.
4. Brudno,M., Do,C., Cooper,G.M., Kim,M.F., Davydov,E., Green,E.D., Sidow,A. and Batzoglou,S. (2003) LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA. Genome Res., 13, 721-731.
5. Bray,N. and Pachter,L. (2004) MAVID: Constrained ancestral alignment of multiple sequences. Genome Res., 14, 693-699.
6. Swofford,D.L., Olsen,G.J., Waddell,P.J. and Hillis,D.M. (1996) Phylogenetic inference. In Hillis,D.M., Moritz,C. and Mable,B.K. (eds), Molecular Systematics, 2nd edn. Sinauer Associates, Sunderland, MA, pp. 407-514.
7. Kumar,S., Tamura,K., Jakobsen,I.B. and Nei,M. (2001) MEGA2: Molecular Evolutionary Genetics Analysis software. Bioinformatics, 17, 1244-1245.
8. Pearson,W.R. and Lipman,D.J. (1988) Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. USA, 85, 2444-2448.
9. Florea,L., Hartzell,G., Zhang,Z., Rubin,G.M. and Miller,W. (1998) A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res., 8, 967-974.