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Items: 1 to 20 of 100

1.

CAIcal: a combined set of tools to assess codon usage adaptation.

Puigbò P, Bravo IG, Garcia-Vallve S.

Biol Direct. 2008 Sep 16;3:38. doi: 10.1186/1745-6150-3-38.

2.

E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI).

Puigbò P, Bravo IG, Garcia-Vallvé S.

BMC Bioinformatics. 2008 Jan 29;9:65. doi: 10.1186/1471-2105-9-65.

3.

The CAI Analyser Package: inferring gene expressivity from raw genomic data.

Ramazzotti M, Brilli M, Fani R, Manao G, Degl'innocenti D.

In Silico Biol. 2007;7(4-5):507-26.

PMID:
18391240
4.

Codon adaptation index as a measure of dominating codon bias.

Carbone A, Zinovyev A, Képès F.

Bioinformatics. 2003 Nov 1;19(16):2005-15.

PMID:
14594704
5.

INCA: synonymous codon usage analysis and clustering by means of self-organizing map.

Supek F, Vlahovicek K.

Bioinformatics. 2004 Sep 22;20(14):2329-30. Epub 2004 Apr 1.

PMID:
15059815
6.

OPTIMIZER: a web server for optimizing the codon usage of DNA sequences.

Puigbò P, Guzmán E, Romeu A, Garcia-Vallvé S.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W126-31. Epub 2007 Apr 16.

7.

RCDI/eRCDI: a web-server to estimate codon usage deoptimization.

Puigbò P, Aragonès L, Garcia-Vallvé S.

BMC Res Notes. 2010 Mar 31;3:87. doi: 10.1186/1756-0500-3-87.

8.

EuGene: maximizing synthetic gene design for heterologous expression.

Gaspar P, Oliveira JL, Frommlet J, Santos MA, Moura G.

Bioinformatics. 2012 Oct 15;28(20):2683-4. doi: 10.1093/bioinformatics/bts465. Epub 2012 Jul 30.

PMID:
22847936
9.

Online synonymous codon usage analyses with the ade4 and seqinR packages.

Charif D, Thioulouse J, Lobry JR, Perrière G.

Bioinformatics. 2005 Feb 15;21(4):545-7. Epub 2004 Sep 16.

PMID:
15374859
10.
11.

PSAT: a web tool to compare genomic neighborhoods of multiple prokaryotic genomes.

Fong C, Rohmer L, Radey M, Wasnick M, Brittnacher MJ.

BMC Bioinformatics. 2008 Mar 26;9:170. doi: 10.1186/1471-2105-9-170.

12.

webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser.

Löytynoja A, Goldman N.

BMC Bioinformatics. 2010 Nov 26;11:579. doi: 10.1186/1471-2105-11-579.

13.

Relative codon adaptation index, a sensitive measure of codon usage bias.

Lee S, Weon S, Lee S, Kang C.

Evol Bioinform Online. 2010 May 5;6:47-55.

14.

Analysis of synonymous codon usage in Zea mays.

Liu H, He R, Zhang H, Huang Y, Tian M, Zhang J.

Mol Biol Rep. 2010 Feb;37(2):677-84. doi: 10.1007/s11033-009-9521-7. Epub 2009 Mar 29.

PMID:
19330534
15.

Genome-wide analysis reveals class and gene specific codon usage adaptation in avian paramyxoviruses 1.

Taylor TL, Dimitrov KM, Afonso CL.

Infect Genet Evol. 2017 Jun;50:28-37. doi: 10.1016/j.meegid.2017.02.004. Epub 2017 Feb 9.

PMID:
28189889
16.

Correlation between Shine--Dalgarno sequence conservation and codon usage of bacterial genes.

Sakai H, Imamura C, Osada Y, Saito R, Washio T, Tomita M.

J Mol Evol. 2001 Feb;52(2):164-70.

PMID:
11231896
17.

Datamonkey: rapid detection of selective pressure on individual sites of codon alignments.

Pond SL, Frost SD.

Bioinformatics. 2005 May 15;21(10):2531-3. Epub 2005 Feb 15.

PMID:
15713735
18.

Molecular evolution of synonymous codon usage in Populus.

Ingvarsson PK.

BMC Evol Biol. 2008 Nov 4;8:307. doi: 10.1186/1471-2148-8-307.

19.

ATGme: Open-source web application for rare codon identification and custom DNA sequence optimization.

Daniel E, Onwukwe GU, Wierenga RK, Quaggin SE, Vainio SJ, Krause M.

BMC Bioinformatics. 2015 Sep 21;16:303. doi: 10.1186/s12859-015-0743-5.

20.

Effects of nucleotide usage on the synonymous codon usage patterns of biofilm-associated genes in Haemophilus parasuis.

Wang LY, Ma LN, Liu YS.

Genet Mol Res. 2016 Jun 10;15(2). doi: 10.4238/gmr.15027226.

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