SeqFIRE: A web application for automated extraction of indel regions and conserved blocks from protein multiple sequence alignments

Nucleic Acids Research

Volumn 40, Issue W1, 2012, Pages

  Ajawatanawong, Pravech ^a   Atkinson, Gemma C ^b   Watson Haigh, Nathan S ^c   MacKenzie, Bryony ^d   Baldauf, Sandra L ^a  

^a UPPSALA UNIVERSITY   (Sweden)

^b UNIVERSITY OF TARTU   (Estonia)

^c AUSTRALIAN WINE RESEARCH INSTITUTE   (Australia)

^d NONE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; AUTOMATION; COMPUTER PROGRAM; CONTROLLED STUDY; DATA ANALYSIS; ENTROPY; INTERMETHOD COMPARISON; INTERNET; ONLINE SYSTEM; PRIORITY JOURNAL; PROTEIN ANALYSIS; QUALITY CONTROL; SEQUENCE ANALYSIS;

EID: 84864446807     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks561     Document Type: Article

References (37)

1. Aniba, M.R., Poch, O. and Thompson, J.D. (2010) Issues in bioinformatics benchmarking: the case study of multiple sequence alignment. Nucleic Acids Res., 38, 7353-7363.
2. Lockwood, C.A. (2007) Adaptation and functional integration in primate phylogenetics. J. Hum. Evol., 52, 490-503.
3. Rokas, A. and Holland, P.W.H. (2000) Rare genomic changes as a tool for phylogenetics. Trends Ecol. Evol., 15, 454-459.
4. Baldauf, S.L. (1999) A search for the origins of animals and fungi: comparing and combining molecular data. Am. Nat., 154, 178-188.
5. de Jong, W.W., van Dijk, M.A.M., Poux, C., Kappeg., van Rheede, T. and Madsen, O. (2003) Indels in protein-coding sequences of Euarchontoglires constrain the rooting of the eutherian tree. Mol. Phylogenet. Evol., 28, 328-340.
6. Rivera, M.C. and Lake, J.A. (1992) Evidence that eukaryotes and eocyte prokaryotes are immediate relatives. Science, 257, 74-76.
7. Cox, C.J., Foster, P.G., Hirt, R.P., Harris, S.R. and Embley, T.M. (2008) The archaebacterial origin of eukaryotes. Proc. Natl Acad. Sci. USA, 105, 20356-20361.
8. Ciccarelli, F.D., Doerks, T., von Mering, C., Creevey, C.J., Snel, B. and Bork, P. (2006) Toward automatic reconstruction of a highly resolved tree of life. Science, 311, 1283-1287.
9. Castresana, J. (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol., 17, 540-552.
10. Talavera, G. and Castresana, J. (2007) Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol., 56, 564-577.
11. Waterhouse, A.M., Procter, J.B., Martin, D.M.A., Clamp, M. and Barton, G.J. (2009) Jalview version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics, 25, 1189-1191.
12. Thorne, J.L. (2000) Models of protein sequence evolution and their applications. Curr. Opin. Genet. Dev., 10, 602-605.
13. Rost, B. (1999) Twilight zone of protein sequence alignments. Protein Eng., 12, 85-94.
14. Kumar, S., Skj?eland, á ., Orr, R.J.S., Enger, P., Ruden, T., Mevik, B.H., Burki, F., Botnen, A. and Shalchian-Tabrizi, K. (2009) AIR: a batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses. BMC Bioinformatics, 10, 357.
15. Hirt, R.P., Logsdon, J.M. Jr, Healy, B., Dorey, M.W., Doolittle, W.F. and Embley, T.M. (1999) Microsporidia are related to fungi: evidence from the largest subunit of RNA polymerase II and other proteins. Proc. Natl Acad. Sci. USA, 96, 580-585.
16. Thompson, J.D., Koehl, P., Ripp, R. and Poch, O. (2005) BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark. Proteins, 61, 127-136.
17. Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
18. Löytynoja, A. and Goldman, N. (2008) Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science, 320, 1632-1635.
19. Wu, M., Chatterji, S. and Eisen, J.A. (2012) Accounting for alignment uncertainty in phylogenomics. PLoS One, 7, e30288.
20. Smagala, J.A., Dawson, E.D., Mehlmann, M., Townsend, M.B., Kuchta, R.D. and Rowlen, K.L. (2005) ConFind: a robust tool for conserved sequence identification. Bioinformatics, 21, 4420-4422.
21. Dunn, C.W., Hejnol, A., Matus, D.Q., Pang, K., Browne, W.E., Smith, S.A., Seaver, E., Rouse, G.W., Obst, M., Edgecombe, G.D. et al. (2008) Broad phylogenomic sampling improves resolution of the animal tree of life. Nature, 452, 745-749.
22. Hackett, J.D., Yoon, H.S., Li, S., Reyes-Prieto, A., Ru?mmele, S.E. and Bhattacharya, D. (2007) Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of rhizaria with chromalveolates. Mol. Biol. Evol., 24, 1702-1713.
23. Hibbett, D.S., Binder, M., Bischoff, J.F., Blackwell, M., Cannon, P.F., Eriksson, O.E., Huhndorf, S., James, T., Kirk, P.M., Lu?cking, R. et al. (2007) A higher-level phylogenetic classification of the Fungi. Mycol. Res., 111, 509-547.
24. Hsing, M. and Cherkasov, A. (2008) Indel PDB: a database of structural insertions and deletions derived from sequence alignments of closely related proteins. BMC Bioinformatics, 9, 293.
25. Zhang, Z., Xing, C., Wang, L., Gong, B. and Liu, H. (2012) IndelFR: a database of indels in protein structures and their flanking regions. Nucleic Acids Res., 40, D512-D518.
26. Chen, F.C., Chen, C.J. and Chuang, T.J. (2007) INDELSCAN: a web server for comparative identification of species-specific and non-species-specific insertion/deletion events. Nucleic Acid Res., 35, W633-W638.
27. Krissinel, E. and Henrick, K. (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr. D Biol. Crystallogr., 60, 2256-2268.
28. Baldauf, S.L. and Palmer, J.D. (1993) Animals and fungi are each other's closest relatives: congruent evidence from multiple proteins. Proc. Natl Acad. Sci. USA, 90, 11558-11562.
29. Belinky, F., Cohen, O. and Huchon, D. (2010) Large-scale parsimony analysis of metazoan indels in protein-coding genes. Mol. Biol. Evol., 27, 441-451.
30. Allard, M.W. and Carpenter, J.M. (1996) On weighting and congruence. Cladistics, 12, 183-198.
31. Milinkovitch, M.C., LeDuc, R.G., Adachi, J., Farnir, F., Georges, M. and Hasegawa, M. (1996) Effects of character weighting and species sampling on phylogeny reconstruction: a case study based on DNA sequence data in cetaceans. Genetics, 144, 1817-1833.
32. Goloboff, P.A., Carpenter, J.M., Arias, J.S. and Esquivel, D.R.M. (2008) Weighting against homoplasy improves phylogenetic analysis of morphological data sets. Cladistics, 24, 1-16.
33. Young, N.D. and Healy, J. (2003) GapCoder automates the use of indel characters in phylogenetic analysis. BMC Bioinformatics, 4, 6.
34. Redelings, B.D. and Suchard, M.A. (2007) Incorporating indel information into phylogeny estimation for rapidly emerging pathogens. BMC Evol. Biol., 7, 40.
35. Simmons, M.P., Müller, K. and Norton, A.P. (2007) The relative performance of indel-coding methods in simulations. Mol. Phylogenet. Evol., 44, 724-740.
36. Simmons, M.P. and Ochoterena, H. (2000) Gaps as characters in sequence-based phylogenetic analyses. Syst. Biol., 49, 369-381.
37. Müller, K. (2005) SeqState: primer design and sequence statistics for phylogenetic DNA datasets. Appl. Bioinformatics, 4, 65-69.