دورية أكاديمية
أعرض في EDS

ALF--a simulation framework for genome evolution.

التفاصيل البيبلوغرافية
العنوان: ALF--a simulation framework for genome evolution.
المؤلفون: Dalquen DA; Computational Biochemistry Research Group, Department of Computer Science, ETH Zurich, Universitätstrasse 6, Zürich, Switzerland. ddalquen@inf.ethz.ch, Anisimova M, Gonnet GH, Dessimoz C
المصدر: Molecular biology and evolution [Mol Biol Evol] 2012 Apr; Vol. 29 (4), pp. 1115-23. Date of Electronic Publication: 2011 Dec 08.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Oxford University Press Country of Publication: United States NLM ID: 8501455 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1537-1719 (Electronic) Linking ISSN: 07374038 NLM ISO Abbreviation: Mol Biol Evol Subsets: MEDLINE
أسماء مطبوعة: Publication: 2003- : New York, NY : Oxford University Press
Original Publication: [Chicago, Ill.] : University of Chicago Press, [c1983-
مواضيع طبية MeSH: Evolution, Molecular* , Genome* , Models, Genetic* , Software*, Computational Biology/*methods, Algorithms ; Base Composition ; Computer Simulation ; Gene Transfer, Horizontal ; Genetic Speciation ; Mutagenesis
مستخلص: In computational evolutionary biology, verification and benchmarking is a challenging task because the evolutionary history of studied biological entities is usually not known. Computer programs for simulating sequence evolution in silico have shown to be viable test beds for the verification of newly developed methods and to compare different algorithms. However, current simulation packages tend to focus either on gene-level aspects of genome evolution such as character substitutions and insertions and deletions (indels) or on genome-level aspects such as genome rearrangement and speciation events. Here, we introduce Artificial Life Framework (ALF), which aims at simulating the entire range of evolutionary forces that act on genomes: nucleotide, codon, or amino acid substitution (under simple or mixture models), indels, GC-content amelioration, gene duplication, gene loss, gene fusion, gene fission, genome rearrangement, lateral gene transfer (LGT), or speciation. The other distinctive feature of ALF is its user-friendly yet powerful web interface. We illustrate the utility of ALF with two possible applications: 1) we reanalyze data from a study of selection after globin gene duplication and test the statistical significance of the original conclusions and 2) we demonstrate that LGT can dramatically decrease the accuracy of two well-established orthology inference methods. ALF is available as a stand-alone application or via a web interface at http://www.cbrg.ethz.ch/alf.
References: Mol Biol Evol. 2009 Feb;26(2):255-71. (PMID: 18922761)
Mol Biol Evol. 1995 Jul;12(4):546-57. (PMID: 7659011)
Mol Biol Evol. 2008 Jul;25(7):1307-20. (PMID: 18367465)
BMC Bioinformatics. 2011 Apr 19;12:104. (PMID: 21504561)
BMC Bioinformatics. 2011 Jan 10;12:11. (PMID: 21219603)
Comput Appl Biosci. 1997 Oct;13(5):559-60. (PMID: 9367131)
Mol Biol Evol. 2001 May;18(5):691-9. (PMID: 11319253)
Comput Appl Biosci. 1997 Oct;13(5):555-6. (PMID: 9367129)
J Theor Biol. 2008 Aug 21;253(4):769-78. (PMID: 18538793)
Bioinformatics. 2005 Sep 15;21(18):3686-7. (PMID: 16020469)
Hum Hered. 2010;70(4):287-91. (PMID: 21212684)
Mol Biol Evol. 2009 Aug;26(8):1879-88. (PMID: 19423664)
BMC Bioinformatics. 2005 Jun 01;6:134. (PMID: 15927081)
Evol Bioinform Online. 2007 Feb 26;1:81-3. (PMID: 19325855)
J Mol Biol. 2001 Dec 14;314(5):1041-52. (PMID: 11743721)
BMC Bioinformatics. 2008 Sep 08;9:364. (PMID: 18778480)
PLoS Comput Biol. 2009 Jan;5(1):e1000262. (PMID: 19148271)
Mol Biol Evol. 1996 Jan;13(1):93-104. (PMID: 8583911)
BMC Bioinformatics. 2008 Dec 04;9:518. (PMID: 19055798)
J Mol Evol. 1985;22(2):160-74. (PMID: 3934395)
Bioinformatics. 2002 Jul;18(7):1015-6. (PMID: 12117802)
BMC Bioinformatics. 2005 Sep 27;6:236. (PMID: 16188037)
Science. 2000 Nov 10;290(5494):1151-5. (PMID: 11073452)
Mol Biol Evol. 1995 May;12(3):451-8. (PMID: 7739387)
Bioinformatics. 2004 Dec 12;20(18):3673-5. (PMID: 15271777)
Brief Bioinform. 2011 Sep;12(5):423-35. (PMID: 21737420)
Genetics. 2007 Nov;177(3):1725-31. (PMID: 17947444)
Mol Biol Evol. 2007 Jul;24(7):1464-79. (PMID: 17400572)
J Mol Biol. 2004 Aug 6;341(2):617-31. (PMID: 15276848)
Proteins. 2001 Oct 1;45(1):102-4. (PMID: 11536366)
J Mol Evol. 2004 Jul;59(1):121-32. (PMID: 15383915)
Syst Biol. 2003 Oct;52(5):696-704. (PMID: 14530136)
Bioinformatics. 2008 Dec 1;24(23):2786-7. (PMID: 18842601)
Genetics. 2000 May;155(1):431-49. (PMID: 10790415)
BMC Evol Biol. 2008 Jun 23;8:179. (PMID: 18573206)
PLoS One. 2011;6(5):e20488. (PMID: 21647374)
Genome Res. 2005 Nov;15(11):1576-83. (PMID: 16251467)
Bioinformatics. 2010 Sep 1;26(17):2200-1. (PMID: 20671150)
J Mol Biol. 1993 Feb 20;229(4):1065-82. (PMID: 8445636)
Appl Bioinformatics. 2003;2(3):159-63. (PMID: 15130802)
Bioinformatics. 2006 Mar 15;22(6):716-22. (PMID: 16332711)
Science. 1992 Jun 5;256(5062):1443-5. (PMID: 1604319)
Bioinformatics. 2002 Feb;18(2):337-8. (PMID: 11847089)
Mol Biol Evol. 2007 Mar;24(3):640-9. (PMID: 17158778)
Bioinformatics. 1998;14(2):157-63. (PMID: 9545448)
Mol Biol Evol. 2008 Apr;25(4):688-95. (PMID: 18192698)
J Mol Biol. 1982 Dec 15;162(3):705-8. (PMID: 7166760)
Mol Biol Evol. 1993 May;10(3):512-26. (PMID: 8336541)
Philos Trans R Soc Lond B Biol Sci. 2009 Aug 12;364(1527):2241-51. (PMID: 19571244)
Bioinformatics. 2007 Apr 1;23(7):825-31. (PMID: 17267425)
Comput Appl Biosci. 1997 Jun;13(3):235-8. (PMID: 9183526)
Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11188-9. (PMID: 14506293)
Bioinformatics. 2005 Nov 1;21 Suppl 3:iii31-8. (PMID: 16306390)
Bioinformatics. 2000 Feb;16(2):101-3. (PMID: 10842729)
J Mol Evol. 1997 Apr;44(4):383-97. (PMID: 9089078)
Philos Trans R Soc Lond B Biol Sci. 2003 Jan 29;358(1429):39-57; discussion 57-8. (PMID: 12594917)
Genome Res. 2008 Mar;18(3):449-61. (PMID: 18230802)
Comput Appl Biosci. 1992 Jun;8(3):275-82. (PMID: 1633570)
تواريخ الأحداث: Date Created: 20111214 Date Completed: 20120919 Latest Revision: 20211021
رمز التحديث: 20231215
مُعرف محوري في PubMed: PMC3341827
DOI: 10.1093/molbev/msr268
PMID: 22160766
قاعدة البيانات: MEDLINE
الوصف
تدمد:1537-1719
DOI:10.1093/molbev/msr268