Literature DB >> 3281142

A backtranslation method based on codon usage strategy.

G Pesole1, M Attimonelli, S Liuni.   

Abstract

This study describes a method for the backtranslation of an aminoacidic sequence, an extremely useful tool for various experimental approaches. It involves two computer programs CLUSTER and BACKTR written in Fortran 77 running on a VAX/VMS computer. CLUSTER generates a reliable codon usage table through a cluster analysis, based on a chi 2-like distance between the sequences. BACKTR produces backtranslated sequences according to different options when use is made of the codon usage table obtained in addition to selecting the least ambiguous potential oligonucleotide probes within an aminoacidic sequence. The method was tested by applying it to 158 yeast genes.

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Year:  1988        PMID： 3281142      PMCID： PMC338166          DOI： 10.1093/nar/16.5.1715

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  13 in total

1.  Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes.

Authors:  T Ikemura
Journal:  J Mol Biol       Date:  1981-02-15       Impact factor: 5.469

2.  ACNUC--a portable retrieval system for nucleic acid sequence databases: logical and physical designs and usage.

Authors:  M Gouy; C Gautier; M Attimonelli; C Lanave; G di Paola
Journal:  Comput Appl Biosci       Date:  1985-09

3.  The codon preference plot: graphic analysis of protein coding sequences and prediction of gene expression.

Authors:  M Gribskov; J Devereux; R R Burgess
Journal:  Nucleic Acids Res       Date:  1984-01-11       Impact factor: 16.971

4.  Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs.

Authors:  T Ikemura
Journal:  J Mol Biol       Date:  1982-07-15       Impact factor: 5.469

5.  Codon usage in bacteria: correlation with gene expressivity.

Authors:  M Gouy; C Gautier
Journal:  Nucleic Acids Res       Date:  1982-11-25       Impact factor: 16.971

6.  Synthetic oligonucleotide probes deduced from amino acid sequence data. Theoretical and practical considerations.

Authors:  R Lathe
Journal:  J Mol Biol       Date:  1985-05-05       Impact factor: 5.469

7.  Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system.

Authors:  T Ikemura
Journal:  J Mol Biol       Date:  1981-09-25       Impact factor: 5.469

8.  Codon selection in yeast.

Authors:  J L Bennetzen; B D Hall
Journal:  J Biol Chem       Date:  1982-03-25       Impact factor: 5.157

Review 9.  Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes.

Authors:  H Grosjean; W Fiers
Journal:  Gene       Date:  1982-06       Impact factor: 3.688
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  9 in total

1.  Detecting positively selected sites from amino Acid sequences: an implicit codon model.

Authors:  Zheng Ouyang; Jie Liang
Journal:  Conf Proc IEEE Eng Med Biol Soc       Date:  2007

2.  The branching order of mammals: phylogenetic trees inferred from nuclear and mitochondrial molecular data.

Authors:  G Pesole; E Sbisá; F Mignotte; C Saccone
Journal:  J Mol Evol       Date:  1991-12       Impact factor: 2.395

3.  Challenges associated with heterologous expression of Flavobacterium psychrophilum proteins in Escherichia coli.

Authors:  Devendra H Shah; Kenneth D Cain; Gregory D Wiens; Douglas R Call
Journal:  Mar Biotechnol (NY)       Date:  2008-06-13       Impact factor: 3.619

4.  The yeast gene MSH3 defines a new class of eukaryotic MutS homologues.

Authors:  L New; K Liu; G F Crouse
Journal:  Mol Gen Genet       Date:  1993-05

5.  Sequence similarity is more relevant than species specificity in probabilistic backtranslation.

Authors:  Alfredo Ferro; Rosalba Giugno; Giuseppe Pigola; Alfredo Pulvirenti; Cinzia Di Pietro; Michele Purrello; Marco Ragusa
Journal:  BMC Bioinformatics       Date:  2007-02-21       Impact factor: 3.169

6.  Lateral gene transfer and ancient paralogy of operons containing redundant copies of tryptophan-pathway genes in Xylella species and in heterocystous cyanobacteria.

Authors:  Gary Xie; Carol A Bonner; Tom Brettin; Raphael Gottardo; Nemat O Keyhani; Roy A Jensen
Journal:  Genome Biol       Date:  2003-01-29       Impact factor: 13.583

7.  Using purine skews to predict genes in AT-rich poxviruses.

Authors:  Melissa Da Silva; Chris Upton
Journal:  BMC Genomics       Date:  2005-02-18       Impact factor: 3.969

8.  The mitochondrial genome of Phallusia mammillata and Phallusia fumigata (Tunicata, Ascidiacea): high genome plasticity at intra-genus level.

Authors:  Fabio Iannelli; Francesca Griggio; Graziano Pesole; Carmela Gissi
Journal:  BMC Evol Biol       Date:  2007-08-31       Impact factor: 3.260

9.  Optimal encoding rules for synthetic genes: the need for a community effort.

Authors:  Gang Wu; Laura Dress; Stephen J Freeland
Journal:  Mol Syst Biol       Date:  2007-09-18       Impact factor: 11.429
  9 in total

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