Understanding the correlation between synonymous substitution rate and GC content is essential to decipher the gene evolution. However, it has been controversial on their relationship. We analyzed the GC content and synonymous substitution rate in 1092 paralogues produced by two large-scale duplication events in the rice genome. According to the GC content at the third codon sites (GC3), the pa...

We examined the pattern of synonymous substitutions in the duplicated Amylase (Amy) genes (called the Amy1- and Amy3-type genes, respectively) in the Drosophila montium species subgroup. The GC content at the third synonymous codon sites of the Amy1-type genes was higher than that of the Amy3-type genes, while the GC content in the 5'-flanking region was the same in both genes. This suggests th...

OBJECTIVE To determine whether synonymous variants in the adenosine triphosphate-binding cassette A3 transporter (ABCA3) gene increase the risk for neonatal respiratory distress syndrome (RDS) in term and late preterm infants of European and African descent. STUDY DESIGN Using next-generation pooled sequencing of race-stratified DNA samples from infants of European and African descent at ≥34 ...

Codon evolutionary models are widely used to infer the selection forces acting on a protein. The non-synonymous to synonymous rate ratio (denoted by Ka/Ks) is used to infer specific positions that are under purifying or positive selection. Current evolutionary models usually assume that only the non-synonymous rates vary among sites while the synonymous substitution rates are constant. This ass...

The Xdh (rosy) region of Drosophila subobscura has been sequenced and compared to the homologous region of D. pseudoobscura and D. melanogaster. Estimates of the numbers of synonymous substitutions per site (Ks) confirm that Xdh has a high synonymous substitution rate. The distributions of both nonsynonymous and synonymous substitutions along the coding region were found to be heterogeneous. Al...

Abstract There are various ways to express the same meaning in natural language. This diversity causes difficulty in many fields of natural language processing. It can be reduced by normalization of synonymous expressions, which is done by replacing various synonymous expressions with a standard one. In this paper, we propose a method for extracting paraphrases from a parallel corpus automatica...