The finding that the ribosome can robustly slide on poly(A) sequences explains bioinformatic analyses revealing that consecutive AAA codons are under-represented in ORFs in all genomes (unpublished data) and helps to rationalize the widespread usage of poly(A) sequence as a regulatory rather than a coding feature.
Finally, we used a CAI calculator to score the codon usage of a gene sequence (Sharp and Li, 1987).
Therefore, we implemented a de novo poly(A) tail detection script to identify reads containing noncanonical poly(A) tails and to ensure the usage of all sequenced bases starting immediately after the poly(A) tail of the RNA molecule they were derived from.
Compared with the 70-80% of CG dinucleotides being methylated in humans [ 11], this proportion is higher, which likely stems from the usage of a methylation site enriched sequence causing a slightly biased over-all methylation rate.
The server first provides a number of basic calculations that are also available elsewhere: (i) The absolute and synonymous codon usage of a group of DNA sequences and other useful parameters such as length, total G+C content and G+C content at the three codon positions, and the effective number of codons [ 17]. (ii) The CAI of a DNA sequence or group of sequences.
Important in all these systems is what determines the frequency of usage of individual sequence donors for recombination into an expression site.
The assembly of ESTs can be expected to generate an overestimate of the actual number of genes represented since failure of ESTs to assemble can result from alternate splicing, differences in usage of polyadenylation sites, sequence polymorphism, and sequencing errors.
The usage of Jungck sequence is here also possible, but becomes more involved.
Ab initio motif-finding and prediction of binding sites using DWMs, and the usage of homologous sequence from related species to improve predictions, are interesting topics that deserves to be addressed in the near future, perhaps as extensions of the PhyloGibbs program [29], [30].
Thus, the usage of ITS2 sequence together with secondary structure for taxonomic inferences is recommended [ 25].
