Analysis of Codon Usage Patterns in Toxic Dinoflagellate Alexandrium tamarense through Expressed Sequence Tag Data

Analysis of Codon Usage Patterns in Toxic Dinoflagellate Alexandrium tamarense through Expressed Sequence Tag Data

We have analyzed synonymous codon usage in the genome of A. tamarense CCMP 1598 for protein-coding sequences from 10865 expressed sequence tags (ESTs). We reconstructed a total of 4284 unigenes, including 74 ribosomal protein and 40 plastid-related genes, from ESTs using FrameDP, an open reading fra...

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Veröffentlicht in:Comparative and functional genomics 2010-01, Vol.2010 (2010), p.1-9
Hauptverfasser: Wong, Tit-Yee, Lin, Chorng-Horng, Liu, Jong-Kang, Kuo, Jimmy, Hsiao, Yi-Yuong
Format: Artikel
Sprache:eng
Schlagworte:
Bias
Bioinformatics
Biology
Codon
Deoxyribonucleic acid
Dinoflagellates
DNA
DNA sequencing
Free radicals
Gene expression
Genetic aspects
Genetics
Genomes
Libraries
Microbiology
Microorganisms
Museum exhibits
Nucleotide sequencing
Organisms
Physiological aspects
Plastids
Prokaryotes
Protein synthesis
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Zusammenfassung:We have analyzed synonymous codon usage in the genome of A. tamarense CCMP 1598 for protein-coding sequences from 10865 expressed sequence tags (ESTs). We reconstructed a total of 4284 unigenes, including 74 ribosomal protein and 40 plastid-related genes, from ESTs using FrameDP, an open reading frame (ORF) prediction program. Correspondence analysis of A. tamarense genes based on codon usage showed that the GC content at the third base of synonymous codons (GC3s) was strongly correlated with the first axis (r=0.93 with P
ISSN:1531-6912
2314-436X
1532-6268
2314-4378
DOI:10.1155/2010/138538