title: Transimulation - protein biosynthesis web service.
abstract: Although translation is the key step during gene expression, it remains poorly characterized at the level of individual genes. For this reason, we developed Transimulation - a web service measuring translational activity of genes in three model organisms: Escherichia coli, Saccharomyces cerevisiae and Homo sapiens. The calculations are based on our previous computational model of translation and experimental data sets. Transimulation quantifies mean translation initiation and elongation time (expressed in SI units), and the number of proteins produced per transcript. It also approximates the number of ribosomes that typically occupy a transcript during translation, and simulates their propagation. The simulation of ribosomes' movement is interactive and allows modifying the coding sequence on the fly. It also enables uploading any coding sequence and simulating its translation in one of three model organisms. In such a case, ribosomes propagate according to mean codon elongation times of the host organism, which may prove useful for heterologous expression. Transimulation was used to examine evolutionary conservation of translational parameters of orthologous genes. Transimulation may be accessed at http://nexus.ibb.waw.pl/Transimulation (requires Java version 1.7 or higher). Its manual and source code, distributed under the GPL-2.0 license, is freely available at the website.
authors.affiliation: Department of Bioinformatics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
authors.forename: Marlena
authors.initials: M
authors.lastname: Siwiak
authors.forename: Piotr
authors.initials: P
authors.lastname: Zielenkiewicz
mesh_terms: D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D006801:Humans; D014176:Protein Biosynthesis / Q000502:physiology*; D011506:Proteins / Q000235:genetics* / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D064878:Web Browser
chemical_list: D011506:Proteins
references.citation: Mol Syst Biol. 2011 Nov 08;7:548
references.pmid: 22068331
references.citation: J Mol Biol. 1996 Aug 2;260(5):649-63
references.pmid: 8709146
references.citation: Biochemistry. 1977 Jun 14;16(12):2783-91
references.pmid: 889788
references.citation: Nature. 2010 Aug 12;466(7308):835-40
references.pmid: 20703300
references.citation: Science. 2010 Jul 30;329(5991):533-8
references.pmid: 20671182
references.citation: Oncogene. 2004 Apr 19;23(18):3248-64
references.pmid: 15094774
references.citation: Proc Natl Acad Sci U S A. 2003 Apr 1;100(7):3889-94
references.pmid: 12660367
references.citation: J Biol Chem. 1986 Oct 15;261(29):13800-6
references.pmid: 3020051
references.citation: Proc Natl Acad Sci U S A. 2002 Apr 30;99(9):5860-5
references.pmid: 11972065
references.citation: J Theor Biol. 2008 Apr 21;251(4):616-27
references.pmid: 18237749
references.citation: Genome Res. 2012 May;22(5):947-56
references.pmid: 22369889
references.citation: Comput Biol Chem. 2007 Oct;31(5-6):335-46
references.pmid: 17897886
references.citation: Structure. 1999 Feb 15;7(2):143-56
references.pmid: 10368282
references.citation: Trends Biochem Sci. 2005 Sep;30(9):506-14
references.pmid: 16054366
references.citation: J Biol Chem. 1981 Mar 10;256(5):2514-21
references.pmid: 7462253
references.citation: Nat Struct Mol Biol. 2008 Dec;15(12):1263-71
references.pmid: 19011635
references.citation: Biochem Biophys Res Commun. 2006 Jan 13;339(2):603-10
references.pmid: 16310166
references.citation: PLoS Comput Biol. 2010 Jul 29;6(7):e1000865
references.pmid: 20686685
references.citation: Mol Syst Biol. 2006;2:2006.0026
references.pmid: 16738570
references.citation: Nucleic Acids Res. 2010 Jan;38(Database issue):D196-203
references.pmid: 19892828
references.citation: Science. 2009 Apr 10;324(5924):218-23
references.pmid: 19213877
references.citation: Biotechnol Bioeng. 1997 Jun 5;54(5):461-7
references.pmid: 18634138
references.citation: Phys Biol. 2008 Nov 07;5(4):046001
references.pmid: 18997273
references.citation: Proc Natl Acad Sci U S A. 2002 Jul 23;99(15):9697-702
references.pmid: 12119387
references.citation: Mol Cell Biol. 1999 Mar;19(3):1720-30
references.pmid: 10022859
references.citation: Cell. 2009 Feb 20;136(4):731-45
references.pmid: 19239892
references.citation: BMC Genomics. 2008 Nov 29;9:574
references.pmid: 19040753
references.citation: J Biol Chem. 1972 Jun 10;247(11):3622-9
references.pmid: 4624122
references.citation: J Mol Biol. 1997 May 2;268(2):322-30
references.pmid: 9159473
references.citation: Nucleic Acids Res. 2010 Jan;38(Database issue):D750-3
references.pmid: 19854939
references.citation: PLoS Genet. 2006 Dec;2(12):e221
references.pmid: 17194224
references.citation: Nat Rev Mol Cell Biol. 2005 Apr;6(4):318-27
references.pmid: 15803138
references.citation: J Biol Chem. 1972 Nov 10;247(21):6770-80
references.pmid: 5082126
references.citation: Lab Chip. 2007 Apr;7(4):423-40
references.pmid: 17389958
references.citation: Nature. 2006 Jun 15;441(7095):840-6
references.pmid: 16699522
references.citation: BMC Syst Biol. 2008 Oct 16;2:87
references.pmid: 18925958
references.citation: Trends Biochem Sci. 1999 Nov;24(11):437-40
references.pmid: 10542411
references.citation: Proc Natl Acad Sci U S A. 2011 Jun 28;108(26):10626-31
references.pmid: 21670266
references.citation: J Biol Chem. 1970 Jun 10;245(11):2889-900
references.pmid: 4912536
references.citation: Mol Cell Proteomics. 2004 Oct;3(10):960-9
references.pmid: 15238602
references.citation: Science. 2002 Jul 19;297(5580):395-400
references.pmid: 12089449
references.citation: NMR Biomed. 2008 Feb;21(2):159-64
references.pmid: 17461436
references.citation: Nature. 2012 Mar 28;484(7395):538-41
references.pmid: 22456704
references.citation: Nat Biotechnol. 2007 Jan;25(1):117-24
references.pmid: 17187058