Literature DB >> 16388144

A new measure to study phylogenetic relations in the brown algal order Ectocarpales: the "codon impact parameter".

Smarajit Das1, Jayprokas Chakrabarti, Zhumur Ghosh, Satyabrata Sahoo, Bibekanand Mallick.   

Abstract

We analyse forty-seven chloroplast genes of the large subunit of RuBisCO, from the algal order Ectocarpales, sourced from GenBank. Codon-usage weighted by the nucleotide base-bias defines our score called the codon-impact-parameter. This score is used to obtain phylogenetic relations amongst the 47 Ectocarpales. We compare our classification with the ones done earlier.

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Year:  2005        PMID： 16388144     DOI： 10.1007/BF02703570

Source DB:  PubMed          Journal:  J Biosci        ISSN： 0250-5991            Impact factor:   1.826


  15 in total

1.  Phylogenetic relationships among algae based on complete large-subunit rRNA sequences.

Authors:  A Ben Ali; R De Baere; G Van der Auwera; R De Wachter; Y Van de Peer
Journal:  Int J Syst Evol Microbiol       Date:  2001-05       Impact factor: 2.747

2.  The neighbor-joining method: a new method for reconstructing phylogenetic trees.

Authors:  N Saitou; M Nei
Journal:  Mol Biol Evol       Date:  1987-07       Impact factor: 16.240

3.  Estimation of evolutionary distances between homologous nucleotide sequences.

Authors:  M Kimura
Journal:  Proc Natl Acad Sci U S A       Date:  1981-01       Impact factor: 11.205

4.  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

5.  Phylogenetic analysis. Models and estimation procedures.

Authors:  L L Cavalli-Sforza; A W Edwards
Journal:  Am J Hum Genet       Date:  1967-05       Impact factor: 11.025

6.  Selection on the codon bias of Chlamydomonas reinhardtii chloroplast genes and the plant psbA gene.

Authors:  B R Morton
Journal:  J Mol Evol       Date:  1996-07       Impact factor: 2.395

7.  ALGAE CONTAINING CHLOROPHYLLS a + c ARE PARAPHYLETIC: MOLECULAR EVOLUTIONARY ANALYSIS OF THE CHROMOPHYTA.

Authors:  Debashish Bhattacharya; Linda Medlin; Patricia O Wainright; Edgardo V Ariztia; Claude Bibeau; Shawn K Stickel; Mitchell L Sogin
Journal:  Evolution       Date:  1992-12       Impact factor: 3.694

8.  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

9.  Codon selection in yeast.

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

10.  Phaeothamniophyceae Classis Nova: A New Lineage of Chromophytes Based upon Photosynthetic Pigments, rbcL Sequence Analysis and Ultrastructure.

Authors:  J Craig Bailey; R R Bidigare; S J Christensen; R A Andersen
Journal:  Protist       Date:  2009-07-13
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  1 in total

1.  Comparative Analysis of Predicted Gene Expression among Crenarchaeal Genomes.

Authors:  Shibsankar Das; Brajadulal Chottopadhyay; Satyabrata Sahoo
Journal:  Genomics Inform       Date:  2017-03-29
  1 in total

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