Progressive multiple sequence alignments from triplets

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Kruspe, Matthias ^a   Stadler, Peter F ^a,b,c,d  

^a UNIVERSITY OF LEIPZIG   (Germany)

^b FRAUNHOFER INSTITUTE FOR CELL THERAPY AND IMMUNOLOGY   (Germany)

^c UNIVERSITY OF VIENNA   (Austria)

^d SANTA FE INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

INSERTIONS AND DELETIONS; MULTIPLE ALIGNMENT; MULTIPLE SEQUENCE ALIGNMENTS; PAIRWISE ALIGNMENT; PHYLOGENETIC NETWORKS; PROGRESSIVE ALIGNMENT; SECONDARY STRUCTURES; SEQUENCE ALIGNMENTS;

NUCLEIC ACIDS;

TOOLS;

RNA;

ACCURACY; ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; MOLECULAR PHYLOGENY; NUCLEOTIDE SEQUENCE; PROTEIN SECONDARY STRUCTURE; RNA SEQUENCE; SCORING SYSTEM; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; STRUCTURAL BIOINFORMATICS; ARTIFICIAL INTELLIGENCE; AUTOMATED PATTERN RECOGNITION; METHODOLOGY;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; PATTERN RECOGNITION, AUTOMATED; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

EID: 34547881463     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-254     Document Type: Article

References (45)

1. The aln3nn software http://www.bioinf.uni-leipzig.de/Software/aln3nn
2. Wang L Jiang T On the Complexity of Multiple Sequence Alignment J Comp Biol 1994 1 337-348
3. Thompson J Higgins D Gibson T 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
4. Hogeweg P Hesper B The alignment of sets of sequences and the construction of phylogenetic trees. An integrated method J Mol Evol 1984 20 175-186 10.1007/BF02257378 6433036
5. Feng D Doolittle R Progressive sequence alignment as a prerequisite to correct phylogenetic trees J Mol Evol 1987 25 351-360 10.1007/BF02603120 3118049
6. Saitou N Nei M The neighbor-joining method: A new method, for reconstructing phylogenetic trees Mol Biol Evol 1987 4 406-425 3447015
7. Sokal RR Michner CD A statistical method for evaluating systematic relationships Univ Kans Sci Bull 1958 38 1409-1438
8. Bryant D Moulton V NeighborNet: An agglomerative method for the construction of planar phylogenetic networks WABI '02: Proceedings of the Second International Workshop on Algorithms in Bioinformatics London, UK: Springer-Verlag 2002 375-391
9. Needleman SB Wunsch CD A general method applicable to the search for similarities in the aminoacid sequences of two proteins J Mol Biol 1970 48 443-452 10.1016/0022-2836(70)90057-4 5420325
10. Dewey TG A sequence alignment algorithm with an arbitrary gap penalty function J Comp Biol 2001 8 177-190 10.1089/106652701300312931
11. Gotoh O An improved algorithm for matching biological sequences J Mol Biol 1982 162 705-708 10.1016/0022-2836(82)90398-9 7166760
12. Gotoh O Alignment of three biological sequences with an efficient traceback procedure J theor Biol 1986 121 327-337 10.1016/ S0022-5193(86)80112-6 3795999
13. Konagurthu A Whisstock J Stuckey P Progressive multiple alignment using sequence triplet optimization and three-residue exchange costs J Bioinf and Comp Biol 2004 2 4 719-745 10.1142/S0219720004000831
14. Myers E Miller W Optimal alignemnts in linear space Bioinformatics 1988 4 11-17 10.1093/bioinformatics/4.1.11
15. Lipman D Altschul S Kececioglu J A tool for multiple sequence alignment Proceedings of the National Academy of Sciences of the United States of America 1989 86 12 4412-4415 287279 2734293 10.1073/pnas.86.12.4412
16. Gupta S Kececioglu J Schaffer A Improving the practical space and time efficiency of the shortest-paths approach to sum-of-pairs multiple sequence alignment Journal of Computational Biology 1995 2 3 459-462 8521275
17. Stoye J Multiple sequence alignment with the divide-and-conquer method Gene Combis 1997 211 45-56
18. Bryant D Moulton V Neighbor-Net: An Agglomerative Method for the Construction of Phylogenetic Networks Mol Biol Evol 2004 21 255-265 10.1093/molbev/msh018 14660700
19. Bryant D Moulton V Consistency of Neighbor-Net Alg Mol Biol 2007 2 1 8 Under review 10.1186/1748-7188-2-8
20. Bandelt HJ Dress AWM Split Decomposition: A New and Useful Approach to Phylogenetic Analysis of Distance Data Mol Phyl Evol 1992 1 242-252 10.1016/1055-7903(92)90021-8
21. Huson DH SplitsTree: Analyzing and visualizing evolutionary data Bioinformatics 1998 14 68-73 10.1093/bioinformatics/14.1.68 9520503
22. Wetzel R Zur Visualisierung abstrakter Ähnlichkeitsbeziehungen PhD thesis Bielefeld University, Germany 1995
23. Hofacker I Fontana W Stadler P Bonhoeffer L Tacker M Schuster P Fast folding and comparison of RNA secondary structures Monatshefte für Chemie 1994 125 167-188 10.1007/BF00818163
24. Hofacker I Fekete M Stadler P Secondary structure prediction for aligned RNA sequences J Mol Evol 2002 319 5 1059-1066
25. The Vienna RNA package http://www.tbi.univie.ac.at/RNA
26. Siebert S Backofen R MARNA: Multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons Bioinformatics 2005 21 3352-3359 10.1093/bioinformatics/bti550 15972285
27. Höchsmann M Töller T Giegerich R Kurtz S Local Similarity in RNA Secondary Structures Proc of the Computational Systems Bioinformatics Conference, Stanford, CA, August 2003 (CSB 2003) 2003 2 159-168
28. Sankoff D Simultaneous solution of the RNA folding, alignment, and proto-sequence problems SIAM J Appl Math 1985 45 810-825 10.1137/0145048
29. Hull Havgaard JH Lyngsø R Stormo GD Gorodkin J Pairwise local structural alignment of RNA sequences with sequence similarity less than 40% Bioinformatics 2005 21 1815-1824 10.1093/bioinformatics/bti279 15657094
30. Mathews DH Turner DH Dynalign: An Algorithm for Finding Secondary Structures Common to Two RNA Sequences J Mol Biol 2002 317 191-203 10.1006/jmbi.2001.5351 11902836
31. Will S Missal K Hofacker IL Stadler PF Backofen R Inferring Non-Coding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering PLoS Comp Biol 2006
32. Bonhoeffer LS McCaskill JS Stadler PF Schuster P RNA Multi-Structure Landscapes. A Study Based on Temperature Dependent Partition Functions Eur Biophys J 1993 22 13-24 10.1007/BF00205808 7685689
33. Dalli D Wilm A Mainz I Steger G STRAL: Progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time Bioinformatcs 2006 22 13 1593-1599 10.1093/bioinformatics/btl142
34. McCaskill J The equilibrium partition function and base pair binding probabilities for RNA secondary structure Biopolymers 1990 29 1105-1119 10.1002/bip.360290621 1695107
35. Stoye J Evers D Meyer F Rose: Generating sequence families Bioinformatics 1998 14 157-163 10.1093/bioinformatics/14.2.157 9545448
36. Thompson J Plewniak F Poch O BAliBASE: A benchmark alignment databse for the evaluation of multiple alignment programs Bioinformatcs 1999 15 78-88
37. Do CB Mahabhashyam MSP Brudno M Batzoglou S PROBCONS: Probabilistic Consistency-based Multiple Sequence Alignment Genome Research 2005 15 330-340 546535 15687296 10.1101/gr.2821705
38. Edgar RC MUSCLE: A multiple sequence alignment method with reduced time and space complexity BMC Bioinformatics 2004 5 517706 15318951
39. Notredame C Higgins D Heringa J T-Coffee: A novel method for multiple sequence alignments Journal of Molecular Biology 2000 302 10964570
40. Katoh K Misawa K Kuma K Miyata T MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform Nucleic Acids Res 2002 30 3059-3066 135756 12136088 10.1093/nar/gkf436
41. Griffiths-Jones S Moxon S Marshall M Khanna A Eddy S Bateman A Rfam: annotating noc-coding RNAs in complete genomes Nucleic Acid Research 2005 33
42. Gardner P Wilm A Washietl S A benchmark of multiple sequence alignment programs upon structural RNAs Nucleic Acids Research 2005 33 2433 1087786 15860779 10.1093/nar/gki541
43. Hertel J Lindemeyer M Missal K Fried C Tanzer A Flamm C Hofacker I Stadler P The Expansion of the Metazoan MicroRNA Repertoire BMC Genomics 2006 7 25 1388199 16480513
44. Hertel J Hofacker IL Stadler PF snoReport: Computational identification of snoRNAs with unknown targets 2007 http://www.bioinf.uni-leipzig.de/ Publications/07wplist.html Submitted; preprint BIOINF 07-003
45. Washietl S Hofacker I Stadler P Fast and reliable prediction of noncoding RNAs PNAS 2005 102 7 2454-2459 548974 15665081 10.1073/ pnas.0409169102