Mind the Gaps: Progress in Progressive Alignment

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 2005 Jul 20

PMID 16027352

Citations 4

Authors

D G Higgins

G Blackshields

I M Wallace

Affiliations

Soon will be listed here.

Citing Articles

Genomic evolution of bovine viral diarrhea virus based on complete genome and individual gene analyses.

Spetter M, Louge Uriarte E, Verna A, Odeon A, Gonzalez Altamiranda E Braz J Microbiol. 2023; 54(3):2461-2469.

PMID: 37217730 PMC: 10485219. DOI: 10.1007/s42770-023-00986-4.

MC64-ClustalWP2: a highly-parallel hybrid strategy to align multiple sequences in many-core architectures.

Diaz D, Esteban F, Hernandez P, Caballero J, Guevara A, Dorado G PLoS One. 2014; 9(4):e94044.

PMID: 24710354 PMC: 3977933. DOI: 10.1371/journal.pone.0094044.

Divergence between the Drosophila pseudoobscura and D. persimilis genome sequences in relation to chromosomal inversions.

Noor M, Garfield D, Schaeffer S, Machado C Genetics. 2007; 177(3):1417-28.

PMID: 18039875 PMC: 2147956. DOI: 10.1534/genetics.107.070672.

A macaque's-eye view of human insertions and deletions: differences in mechanisms.

Kvikstad E, Tyekucheva S, Chiaromonte F, Makova K PLoS Comput Biol. 2007; 3(9):1772-82.

PMID: 17941704 PMC: 1976337. DOI: 10.1371/journal.pcbi.0030176.

References

Henikoff S, Henikoff J . Position-based sequence weights. J Mol Biol. 1994; 243(4):574-8. DOI: 10.1016/0022-2836(94)90032-9. View

Altschul S . Gap costs for multiple sequence alignment. J Theor Biol. 1989; 138(3):297-309. DOI: 10.1016/s0022-5193(89)80196-1. View

Notredame C, Higgins D, Heringa J . T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol. 2000; 302(1):205-17. DOI: 10.1006/jmbi.2000.4042. View

Hogeweg P, Hesper B . The alignment of sets of sequences and the construction of phyletic trees: an integrated method. J Mol Evol. 1984; 20(2):175-86. DOI: 10.1007/BF02257378. View

Mizuguchi K, Deane C, Blundell T, Overington J . HOMSTRAD: a database of protein structure alignments for homologous families. Protein Sci. 1998; 7(11):2469-71. PMC: 2143859. DOI: 10.1002/pro.5560071126. View

KROGH A, Brown M, Mian I, Sjolander K, Haussler D . Hidden Markov models in computational biology. Applications to protein modeling. J Mol Biol. 1994; 235(5):1501-31. DOI: 10.1006/jmbi.1994.1104. View

Cline M, Hughey R, Karplus K . Predicting reliable regions in protein sequence alignments. Bioinformatics. 2002; 18(2):306-14. DOI: 10.1093/bioinformatics/18.2.306. View

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 Res. 1994; 22(22):4673-80. PMC: 308517. DOI: 10.1093/nar/22.22.4673. View

Edgar R . MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004; 32(5):1792-7. PMC: 390337. DOI: 10.1093/nar/gkh340. View

10.

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(14):3059-66. PMC: 135756. DOI: 10.1093/nar/gkf436. View

11.

Gardner P, Wilm A, Washietl S . A benchmark of multiple sequence alignment programs upon structural RNAs. Nucleic Acids Res. 2005; 33(8):2433-9. PMC: 1087786. DOI: 10.1093/nar/gki541. View

12.

Thompson J, Plewniak F, Poch O . A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res. 1999; 27(13):2682-90. PMC: 148477. DOI: 10.1093/nar/27.13.2682. View

13.

Do C, Mahabhashyam M, Brudno M, Batzoglou S . ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res. 2005; 15(2):330-40. PMC: 546535. DOI: 10.1101/gr.2821705. View

14.

Taylor W . A flexible method to align large numbers of biological sequences. J Mol Evol. 1988; 28(1-2):161-9. DOI: 10.1007/BF02143508. View

15.

NEEDLEMAN S, Wunsch C . A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol. 1970; 48(3):443-53. DOI: 10.1016/0022-2836(70)90057-4. View

16.

Feng D, Doolittle R . Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J Mol Evol. 1987; 25(4):351-60. DOI: 10.1007/BF02603120. View

17.

Loytynoja A, Goldman N . An algorithm for progressive multiple alignment of sequences with insertions. Proc Natl Acad Sci U S A. 2005; 102(30):10557-62. PMC: 1180752. DOI: 10.1073/pnas.0409137102. View

18.

Smith T, Waterman M . Identification of common molecular subsequences. J Mol Biol. 1981; 147(1):195-7. DOI: 10.1016/0022-2836(81)90087-5. View