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M-Coffee: combining multiple sequence alignment methods with T-Coffee.
Wallace IM, O'Sullivan O, Higgins DG, Notredame C. Wallace IM, et al. Nucleic Acids Res. 2006 Mar 23;34(6):1692-9. doi: 10.1093/nar/gkl091. Print 2006. Nucleic Acids Res. 2006. PMID: 16556910 Free PMC article.
Supervised multivariate analysis of sequence groups to identify specificity determining residues.
Wallace IM, Higgins DG. Wallace IM, et al. BMC Bioinformatics. 2007 Apr 23;8:135. doi: 10.1186/1471-2105-8-135. BMC Bioinformatics. 2007. PMID: 17451607 Free PMC article.
Analysis and comparison of benchmarks for multiple sequence alignment.
Blackshields G, Wallace IM, Larkin M, Higgins DG. Blackshields G, et al. Among authors: wallace im. In Silico Biol. 2006;6(4):321-39. In Silico Biol. 2006. PMID: 16922695
Evaluation of iterative alignment algorithms for multiple alignment.
Wallace IM, O'Sullivan O, Higgins DG. Wallace IM, et al. Bioinformatics. 2005 Apr 15;21(8):1408-14. doi: 10.1093/bioinformatics/bti159. Epub 2004 Nov 25. Bioinformatics. 2005. PMID: 15564300
AVAILABILITY: All of the scripts are freely available on the web at http://www.bioinf.ucd.ie/people/iain/iteration.html CONTACT: iain.wallace@ucd.ie....
AVAILABILITY: All of the scripts are freely available on the web at http://www.bioinf.ucd.ie/people/iain/iteration.html CONTACT: iain.wal
Multiple sequence alignments.
Wallace IM, Blackshields G, Higgins DG. Wallace IM, et al. Curr Opin Struct Biol. 2005 Jun;15(3):261-6. doi: 10.1016/j.sbi.2005.04.002. Curr Opin Struct Biol. 2005. PMID: 15963889 Review.
The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods.
Moretti S, Armougom F, Wallace IM, Higgins DG, Jongeneel CV, Notredame C. Moretti S, et al. Among authors: wallace im. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W645-8. doi: 10.1093/nar/gkm333. Epub 2007 May 25. Nucleic Acids Res. 2007. PMID: 17526519 Free PMC article.
Biol. 2000; 302: 205-217); Wallace, O'Sullivan, Higgins and Notredame (M-Coffee: combining multiple sequence alignment methods with T-Coffee. ...
Biol. 2000; 302: 205-217); Wallace, O'Sullivan, Higgins and Notredame (M-Coffee: combining multiple sequence alignment methods with T …
Fast embedding methods for clustering tens of thousands of sequences.
Blackshields G, Larkin M, Wallace IM, Wilm A, Higgins DG. Blackshields G, et al. Among authors: wallace im. Comput Biol Chem. 2008 Aug;32(4):282-6. doi: 10.1016/j.compbiolchem.2008.03.005. Epub 2008 Mar 26. Comput Biol Chem. 2008. PMID: 18450519
Mind the gaps: progress in progressive alignment.
Higgins DG, Blackshields G, Wallace IM. Higgins DG, et al. Among authors: wallace im. Proc Natl Acad Sci U S A. 2005 Jul 26;102(30):10411-2. doi: 10.1073/pnas.0504801102. Epub 2005 Jul 18. Proc Natl Acad Sci U S A. 2005. PMID: 16027352 Free PMC article. No abstract available.
Clustal W and Clustal X version 2.0.
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. Larkin MA, et al. Among authors: wallace im. Bioinformatics. 2007 Nov 1;23(21):2947-8. doi: 10.1093/bioinformatics/btm404. Epub 2007 Sep 10. Bioinformatics. 2007. PMID: 17846036
Compound prioritization methods increase rates of chemical probe discovery in model organisms.
Wallace IM, Urbanus ML, Luciani GM, Burns AR, Han MK, Wang H, Arora K, Heisler LE, Proctor M, St Onge RP, Roemer T, Roy PJ, Cummins CL, Bader GD, Nislow C, Giaever G. Wallace IM, et al. Chem Biol. 2011 Oct 28;18(10):1273-83. doi: 10.1016/j.chembiol.2011.07.018. Chem Biol. 2011. PMID: 22035796 Free PMC article.
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