The program computes elongation efficiency index (EEI) in five different forms (Likhoshvai VA, Matushkin YG: FEBS Letters 2002) for ribosomal genes within whole genomes. This allows to estimate the role of codon usage bias and potential secondary structures in elongation of translation.
EEI-Calculator uploads flat files with genome sequence (GenBank or EMBL format), extracts all CDS, and automatically recognizes genes involved in ribosomal subunit formation. Means of relative EEI values (M1,..,M5) are then computed for ribosomal genes, with each of five EEI forms. Ribosomal genes are normally highly-expressed in unicellular organisms, and their high M values indicate a positive correlation between EEI index and gene expression. The i-number of the highest Mi (i=1,..,5) corresponds to the main type of translational index. The main type determines main roles of codon composition and/or secondary structures in elongation:
1. codon composition
2. number and length of local hairpins
3. number, length and energy of local hairpins
4. codon composition + number and length of hairpins
5. codon composition + number, length and energy of hairpins
The EEI-Calculator may be applied in general analysis of translational characteristics of poorly investigated genomes, especially in unicellular organisms, where nucleotide composition of CDS is known to play important role in gene expression due to translational effects.
In particular, EC allows to estimate whether gene expression in given organism is correlated with selection towards preferred codons (high M1), or not. This knowledge may be useful in planning transgenic studies with recently sequenced unicellular organisms.
Upload a demo-genome: Escherichia coli K 12 (example)
For details, please see Tutorial