CSA: An efficient algorithm to improve circular DNA multiple alignment

BMC Bioinformatics

Volumn 10, Issue , 2009, Pages

  Fernandes, Francisco ^a,d   Pereira, Luísa ^b,c   Freitas, Ana T ^a,d  

^a INESC ID   (Portugal)

^b UNIVERSITY OF PORTO   (Portugal)

^c University of Porto   (Portugal)

^d INSTITUTO SUPERIOR TÉCNICO   (Portugal)

Author keywords

[No Author keywords available]

Indexed keywords

COMPARATIVE GENOMICS; EVOLUTIONARY HISTORY; EVOLUTIONARY INFORMATION; HOMOLOGOUS SEQUENCES; MULTIPLE SEQUENCE ALIGNMENT ALGORITHM; MULTIPLE SEQUENCE ALIGNMENTS; PHYLOGENETIC ANALYSIS; PHYLOGENETIC COMPARISONS;

DNA; DNA SEQUENCES; ERRORS; GENES; TOOLS;

EVOLUTIONARY ALGORITHMS;

CIRCULAR DNA; MITOCHONDRIAL DNA;

ALGORITHM; ARTICLE; CONTROLLED STUDY; DNA SEQUENCE; GENETIC VARIABILITY; GENOMICS; INFORMATION PROCESSING; MOLECULAR PHYLOGENY; NUCLEOTIDE SEQUENCE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SPECIES COMPARISON; BIOLOGY; CHEMISTRY; COMPUTER PROGRAM; GENETIC DATABASE; METHODOLOGY;

ALGORITHMS; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DNA, CIRCULAR; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 68949145849     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-230     Document Type: Article

References (26)

1. Chenna R Sugawara H Koike T Lopez R Gibson TJ Higgins DG Thompson JD Multiple sequence alignment with the Clustal series of programs Nucleic Acids Res 2003, 31:3497-3500 168907 12824352
2. Thompson JD Higgins DG Gibson TJ CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice Nucleic Acids Res 1994, 22:4673-4680 308517 7984417
3. Notredame C Higgins DG Heringa J T-Coffee: A novel method for fast and accurate multiple sequence alignment J Mol Biol 2000, 302(1):205-17 10964570
4. Brudno M Chapman M Göttgens B Batzoglou S Morgenstern B Fast and sensitive multiple alignment of large genomic sequences BMC Bioinformatics 2003, 4:66 521198 14693042
5. Edgar RC MUSCLE: Multiple sequence alignment with high accuracy and high throughput Nucleic Acids Res 2004, 32(5):1792-1797 390337 15034147
6. Brudno M Do CB Cooper GM Kim MF Davydov E Green ED Sidow A Batzoglou S LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA Genome Res 2003, 13(4):721-731 430158 12654723
7. Bray N Pachter L MAVID: Constrained ancestral alignment of multiple sequences Genome Res 2004, 14:693-699 383315 15060012
8. Darling AC Mau B Blattner FR Perna NT Mauve: Multiple alignment of conserved genomic sequence with rearrangements Genome Res 2004, 14:1394-1403 442156 15231754
9. Castresana J Cytochrome b phylogeny and the taxonomy of great apes and mammals Mol Biol Evol 2001, 18:465-471 11264397
10. Richards M Macaulay V Hickey E Vega E Sykes B Guida V Rengo C Sellitto D Cruciani F Kivisild T Villems R Thomas M Rychkov S Rychkov O Rychkov Y Gölge M Dimitrov D Hill E Bradley D Romano V Calì F Vona G Demaine A Papiha S Triantaphyllidis C Stefanescu G Hatina J Belledi M Di Rienzo A Novelletto A Oppenheim A Nørby S Al-Zaheri N Santachiara-Benerecetti S Scozari R Torroni A Bandelt HJ Tracing European founder lineages in the Near Eastern mtDNA pool Am J Hum Genet 2000, 67:1251-1276 1288566 11032788
11. Pereira L Freitas F Fernandes V Pereira JB Costa MD Costa S Máximo V Macaulay V Rocha R Samuels DC The diversity present in 5,140 human mitochondrial genomes Am J Hum Genet 2009, 84:628-640 19426953
12. Goios A Pereira L Bogue M Macaulay V Amorim A mtDNA phylogeny and evolution of laboratory mouse strains Genome Res 2007, 17:293-298 1800920 17284675
13. Benson DA Karsch-Mizrachi I Lipman DJ Ostell J Wheeler DL GenBank Nucleic Acids Res 2008, 36: Database D25-30 2238942 18073190
14. Pruitt KD Tatusova T Maglott DR NCBI reference sequences (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins Nucleic Acids Res 2007, 35: Database D61-65 1716718 17130148
15. Anderson S Bankier AT Barrell BG de Bruijn MH Coulson AR Drouin J Eperon IC Nierlich DP Roe BA Sanger F Schreier PH Smith AJ Staden R Young IG Sequence and organization of the human mitochondrial genome Nature 1981, 290:457-465 7219534
16. Maes M On a cyclic string-to-string correction problem Inform Process Lett 1990, 35(2):73-78
17. Mollineda RA Vidal E Casacuberta F Cyclic sequence alignments: approximate versus optimal techniques Int J Patt Recogn and Artificial Intelligence 2002, 16(3):291-299
18. Bunke H Bühler U Applications of approximate string matching to 2D shape recognition Patt Recogn 1993, 26(12):1797-1812
19. Mollineda RA Vidal E Casacuberta F Efficient techniques for a very accurate measurement of dissimilarities between cyclic patterns Advances in Pattern Recognition Lecture Notes in Computer Science. Springer 2000, 1876:337-346
20. Fritzsch G Schlegel M Stadler PF Alignments of Mitochondrial Genome Arrangements: Applications to Metazoan Phylogeny J Theor Biol 2006, 240:511-520 16325206
21. Mosig A Hofacker IL Stadler PF Comparative Analysis of Cyclic Sequences: Viroids and other Small Circular RNAs Proceedings of the German Conference on Bioinformatics: 20-22 September 2006; Tübingen P-83:93-102
22. Weiner P Linear Pattern Matching Algorithm Proceedings of the 14th Annual IEEE Symposium on Switching and Automata Theor: 15-17 October 1973; Iowa 1973:1-11
23. Gusfield D Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology New York: Cambridge University Press 1997
24. Ukkonen E On-line Construction of Suffix Trees Algorithmica 1995, 14(3):249-260
25. Excoffier L Laval G Schneider S Arlequin ver. 3.0: An integrated software package for population genetics data analysis Evolutionary Bioinformatics Online 2005, 1:47-50 2658868 19325852
26. Shih AC Lee DT Lin L Peng CL Chen SH Wu YW Wong CY Chou MY Shiao TC Hsieh MF SinicView: A visualization environment for comparisons of multiple nucleotide sequence alignment tools BMC Bioinformatics 2006, 7:103 1434773 16509994