doi: 10.1016/s1046-2023(03)00200-7.
Computational analysis of evolution and conservation in a protein superfamily
Affiliations
- PMID: 14698621
- DOI: 10.1016/s1046-2023(03)00200-7
Item in Clipboard
Computational analysis of evolution and conservation in a protein superfamily
Methods.
2004 Feb.
Abstract
Many gene superfamilies have hundreds or thousands of members and hence pose a significant challenge when performing a large-scale phylogenetic analysis. Derivation of the most accurate alignment possible and inference of evolutionary relationships (with an appropriate measure of confidence) are significant "bottlenecks" in the process. A generally applicable strategy is outlined for identifying and aligning sequences, performing simple analysis of the resulting alignment, and inferring evolutionary relationships. Reference is made to the serpin superfamily. The 'partition cluster' method, a relatively rapid technique for extracting underlying associations from phylogenetic bootstrap trees, is also presented.
Similar articles
-
Phylogeny of the serpin superfamily: implications of patterns of amino acid conservation for structure and function.Genome Res. 2000 Dec;10(12):1845-64. doi: 10.1101/gr.gr-1478r. Genome Res. 2000. PMID: 11116082
-
The ovalbumin serpins revisited: perspective from the chicken genome of clade B serpin evolution in vertebrates.Proc Natl Acad Sci U S A. 2005 Aug 9;102(32):11367-72. doi: 10.1073/pnas.0502934102. Epub 2005 Jul 29. Proc Natl Acad Sci U S A. 2005. PMID: 16055559 Free PMC article.
-
Mulan: multiple-sequence local alignment and visualization for studying function and evolution.Genome Res. 2005 Jan;15(1):184-94. doi: 10.1101/gr.3007205. Epub 2004 Dec 8. Genome Res. 2005. PMID: 15590941 Free PMC article.
-
Multiple sequence alignment.Curr Opin Struct Biol. 2006 Jun;16(3):368-73. doi: 10.1016/j.sbi.2006.04.004. Epub 2006 May 5. Curr Opin Struct Biol. 2006. PMID: 16679011 Review.
-
Inferring trees.Methods Mol Biol. 2008;452:287-309. doi: 10.1007/978-1-60327-159-2_14. Methods Mol Biol. 2008. PMID: 18566770 Review.
Cited by
-
Prospects for inferring very large phylogenies by using the neighbor-joining method.Proc Natl Acad Sci U S A. 2004 Jul 27;101(30):11030-5. doi: 10.1073/pnas.0404206101. Epub 2004 Jul 16. Proc Natl Acad Sci U S A. 2004. PMID: 15258291 Free PMC article.
-
Serpins in plants and green algae.Funct Integr Genomics. 2008 Feb;8(1):1-27. doi: 10.1007/s10142-007-0059-2. Epub 2007 Nov 6. Funct Integr Genomics. 2008. PMID: 18060440 Review.
-
A comparative analysis of serpin genes in the silkworm genome.Genomics. 2009 Apr;93(4):367-75. doi: 10.1016/j.ygeno.2008.12.010. Epub 2009 Jan 16. Genomics. 2009. PMID: 19150649 Free PMC article.
-
Cloning and expression of the major secreted cathepsin B-like protein from juvenile Fasciola hepatica and analysis of immunogenicity following liver fluke infection.Infect Immun. 2003 Dec;71(12):6921-32. doi: 10.1128/IAI.71.12.6921-6932.2003. Infect Immun. 2003. PMID: 14638781 Free PMC article.
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
