To model protein-nucleic acid interactions, it is important to identify the DNA or RNA-binding residues in proteins. Protein sequence features, including the biochemical property of amino acids and evolutionary
Schematics of DNA and RNA structures.AThe canonical right handed double helix, also known as B DNA secondary structure.BZ-DNA forms a left-handed double helix.CG-quadruplexes are formed by the stacking of multiple G-quartets held together by Hoogsteen hydrogen bonds (top). Four guanines establis...
The field of microbiome research has evolved rapidly over the past few decades and has become a topic of great scientific and public interest. As a result of this rapid growth in interest covering different fields, we are lacking a clear commonly agreed definition of the term “microbiome.” M...
With the rapid emergence of RNA databases and newly identified non-coding RNAs, an efficient compression algorithm for RNA sequence and structural information is needed for the storage and analysis of such data. Although several algorithms for compressing DNA sequences have been proposed, none of the...
DNA salvage pathway. TK1 upregulation has been found to be an early event in cancer development. In addition, serum levels of TK1 have been shown to be tied to cancer stage, so that higher levels of TK1 indicate a more serious prognosis. As a result of these findings and others, TK1 ...
Elevated sequencing error rates are the most predominant obstacle in single-nucleotide polymorphism (SNP) detection, which is a major goal in the bulk of current studies using next-generation sequencing (NGS). Beyond routinely handled generic sources of
In the past decades, DNA microarrays have been used extensively to quantify the abundance of mRNA corresponding to different genes, and more recently high-throughput sequencing of cDNA (RNA-seq) has emerged as a powerful competitor. As the cost of sequencing decreases, it is conceivable that the...
of this powerful algorithm [20,25–28]. The first adaptation of the mean shift algorithm to clustering DNA sequences resulted in clusters of better quality than those produced byCD-HITandUCLUST[20]. This adaptation is not the orthodox implementation of the mean shift algorithm. What prevented ...
Secondly, both UAR codons (UAG and UAA) always experience the same alteration of their meaning in nuclear genomes. Reading UAA as a sense codon while keeping UAG as a termination one copes with the problem of the UUA anticodon recognizing not only the UAA codon, but also UAG due to wobble...
Endogenous expression of L1 mRNA is the first step in an L1-initiated mutagenesis event. However, the contribution of individual cell types to patterns of organ-specific L1 mRNA expression remains poorly understood, especially at single-locus resolution.