Grammar-based distance in progressive multiple sequence alignment

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Russell, David J ^a   Otu, Hasan H ^b   Sayood, Khalid ^a  

^a UNIVERSITY OF NEBRASKA LINCOLN   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL SEQUENCES; COMPUTATIONALLY EFFICIENT; GRAMMAR-BASED DISTANCES; LARGE DATASETS; MULTIPLE ALIGNMENT; MULTIPLE SEQUENCE ALIGNMENT ALGORITHM; MULTIPLE SEQUENCE ALIGNMENTS; PROGRESSIVE ALIGNMENT;

AMINO ACIDS;

ALGORITHMS;

AMINO ACID;

AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; GENETIC ALGORITHM; GENETIC DATABASE; GENETIC DISTANCE; GRAMMAR; MATHEMATICAL COMPUTING; MOLECULAR BIOLOGY; SEQUENCE ALIGNMENT; VALIDATION PROCESS; ANIMAL; COMPUTER ANALYSIS; DNA SEQUENCE; GENOMICS; HUMAN; INFORMATION SCIENCE; METHODOLOGY; NATURAL LANGUAGE PROCESSING; NOMENCLATURE; SEMANTICS; SEQUENCE ANALYSIS;

ANIMALS; COMPUTING METHODOLOGIES; DATABASES, GENETIC; GENOMICS; HUMANS; INFORMATION THEORY; NATURAL LANGUAGE PROCESSING; SEMANTICS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, PROTEIN; TERMINOLOGY AS TOPIC;

EID: 47949119484     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-306     Document Type: Article

References (30)

1. Clote P Backofen R Computational Molecular Biology, An Introduction New York, NY: Cambridge University Press 1998
2. Durbin R Eddy S Krogh A Mitchison G Biological Sequence Analysis, Probabilistic Models of Proteins and Nucleic Acids New York, NY: Cambridge University Press 1998
3. Edgar RC Batzoglou S Multiple Sequence Alignment Current Opinion in Structural Biology 2006, 16:368-373 10.1016/j.sbi.2006.04.004 16679011
4. Mitrophanov AY Borodovsky M Statistical Significance in Biological Sequence Analysis Briefings in Bioinformatics 2006, 7:2-24 10.1093/bib/ bbk001 16761361
5. Lipman DJ Altschul SF Kececioglu JD A Tool for Multiple Sequence Alignment Proc Natl Acad Sci USA 1989, 86(12):4412-4415 287279 2734293 10.1073/pnas.86.12.4412
6. Notredame C Recent Evolutions of Multiple Sequence Alignment Algorithms PLoS Computational Biology 2007, 3(8):1405-1408 10.1371/ journal.pcbi.0030123
7. Simossis VA Heringa J PRALINE: A Multiple Seqeunce Alignment Toolbox that Inegrates Homology-Extended and Secondary Structure Information Nucleic Acids Research 2005, 33(Web Server):W289-W294 1160151 15980472 10.1093/nar/gki390
8. Do CB Mahabhashyam MSP Brudno M Batzoglou S ProbCons: Probabilistic Consistency-Based Multiple Sequence Alignment Genome Research 2005, 15(2):330-340 546535 15687296 10.1101/gr.2821705
9. Katoh K Misawa K Kuma K Miyata T MAFFT: A Novel Method for Rapid Multiple Sequence Alignment Based on Fast Fourier Transform Nucleic Acids Research 2002, 30(14):3059-3066 135756 12136088 10.1093/nar/gkf436
10. Katoh K Kuma K Toh H Miyata T MAFFT version 5: Improvement in Accuracy of Multiple Sequence Alignment Nucleic Acids Research 2005, 33(2):511-518 548345 15661851 10.1093/nar/gki198
11. Edgar RC MUSCLE: Multiple Sequence Alignment with High Accuracy and High Throughput Nucleic Acids Research 2004, 32(5):1792-1797 390337 15034147 10.1093/nar/gkh340
12. Edgar RC MUSCLE: A Multiple Sequence Alignment Method with Reduced Time and Space Complexity BMC Bioinformatics 2004, 5(113) 517706 15318951
13. Notredame C Higgins DG Heringa J T-Coffee: A Novel Method for Fast and Accurate Multiple Sequence Alignment Journal of Molecular Biology 2000, 302:205-217 10.1006/jmbi.2000.4042 10964570
14. Lassmann T Sonnhammer E Kalign - an Accurate and Fast Multiple Sequence Alignment Algorithm BMC Bioinformatics 2005, 6(298) 1325270 16343337
15. Sze S Lu Y Yang Q A Polynomial Time Solvable Formulation of Multiple Sequence Alignment Journal of Computational Biology 2006, 13(2):309-319 10.1089/cmb.2006.13.309 16597242
16. Thompson JD Higgins DG Gibson TJ CLUSTAL W: Improving the Sensitivity of Progressive Multiple Sequence Alignment Through Sequence Weighting, Position-Specific Gap Penalties and Weight Matrix Choice Nucleic Acids Research 1994, 22(22):4673-4680 308517 7984417 10.1093/nar/22.22.4673
17. Sundquist A Ronaghi M Tang H Pevzner P Batzoglou S Whole-Genome Sequencing and Assembly with High-Throughput, Short-Read Technologies PLoS ONE 2007, 2(5) 1871613 17534434
18. Ziv J Lempel A A Universal Algorithm for Sequential Data Compression IEEE Transactions on Information Theory 1977, 23:337-343 10.1109/ TIT.1977.1055714
19. Ziv J Lempel A Compression of Individual Sequences via Variable-Rate Coding IEEE Transactions on Information Theory 1978, 24:530-536 10.1109/ TIT.1978.1055934
20. Otu HH Sayood K A New Sequence Distance Measure for Phylogenetic Tree Construction Bioinformatics 2003, 19(16):2122-2130 10.1093/ bioinformatics/btg295 14594718
21. Gusev VD Nemytikova LA Chuzhanova NA On the Complexity Measures of Genetic Sequences Bioinformatics 1999, 15(12):994-999 10.1093/ bioinformatics/15.12.994 10745989
22. Albertson MO Hutchinson JP Discrete Mathematics with Algorithms New York: John Wiley & Sons, Inc 1988
23. Needleman SB Wunsch CD A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins Journal of Molecular Biology 1970, 48(3):443-453 10.1016/0022-2836(70)90057-4 5420325
24. Dayhoff MO Schwartz RM Orcutt BC Atlas of Protein Sequence and Structure, National Biomedical Research Foundation, 1978 chap. A Model of Evolutionary Change in Proteins 5, 345-352
25. Henikoff S Henikoff JG Amino acid substitution matrices from protein blocks Proc Natl Acad Sci USA 1992, 89:10915-10919 50453 1438297 10.1073/ pnas.89.22.10915
26. Gonnet GH Cohen MA Benner SA Exhaustive matching of the entire protein sequence database Science 1992, 256(5062):1443-1445 10.1126/ science.1604319 1604319
27. Thompson JD Plewniak F Poch O BAliBASE: A benchmark alignment database for the evaluation of multiple alignment programs Bioinformatics 1999, 15:87-88 10.1093/bioinformatics/15.1.87 10068696
28. Stoye J DEvers Meyer F Rose: Generating Sequence Families Bioinformatics 1998, 14(2):157-163 10.1093/bioinformatics/14.2.157 9545448
29. Nuin PA Wang Z Tillier ER The Accuracy of Several Multiple Sequence Alignment Programs for Proteins BMC Bioinformatics 2006, 7(471) 1633746 17062146
30. Katoh K Toh H PartTree: An Algorithm to Build an Approximate Tree from a Large Number of Unaligned Sequences Bioinformatics 2007, 23(3):372-374 10.1093/bioinformatics/btl592 17118958