The sequence of the DNA of the origin region of NTP1 has been obtained. Analysis of the sequence indicates that: (1) there is great sequence homology in the DNA upstream from the origin in NTP1, ColE1, CLODF13, PBR345 AND PBR322; (2) only seven base pairs of NTP1 are identical with the sequence downstream from the origin in ColE1, although some homology exists for 140 bases downstream; (3) two ...

Since the discovery of the variety of functional roles performed by nonprotein-coding RNA (ncRNA), the search for homologous RNAs has been a problem of great interest in the field of bioinformatics. This thesis presents a new technique that uses an index-bases search tool to perform RNA homology search. A multiple sequence alignment of an RNA family is used to generate search patterns/descripto...

The traditional base state with amendments model usually use the time sequence when choosing the base state to manipulate and it is usually use the extension of time point to represent the time-slot retrieval, which ignores the adjacent feature of the time point in a certain time-slot. The concept of operated base state and operation times is introduce in this paper, in which a base state with ...

The nucleotide sequence of phoR, the positive and negative regulatory gene for alkaline phosphatase and phosphodiesterase formation in Bacillus subtilis, was determined. The sequence data predicted an open reading frame of 1,740 base pairs (579 amino acids) which overlaps the 5 base pairs of the preceding phoP coding sequence. The deduced amino acid sequence was significantly homologous with th...

Establishing the pattern in peak heights within local sequence contexts improves the accuracy of base calling and the identification of DNA sequence variations in dye-terminator cycle sequencing. We have systematically examined pairs of sequence-tagged sites (STSs) that vary at only a single nucleotide to determine how base changes influence the peak heights of neighboring bases in sequencing t...

In this lecture we discuss gene recognition, i.e., given a sequence of DNA, how can we find the regions in this sequence that encode genes? Gene recognition is at the heart of computational genomics, because simply knowing the base sequence does not reveal anything about the functionality of the DNA. The proteins that an organism can produce are encoded in the base sequence as genes, and we wil...

Traditional sequence analysis depends on sequence alignment. In this study, we analyzed various functional regions of the human genome based on sequence features, including word frequency, dinucleotide relative abundance, and base-base correlation. We analyzed the human chromosome 22 and classified the upstream, exon, intron, downstream, and intergenic regions by principal component analysis an...

RNA polymers are constructed from four distinct nucleotide bases. The sequence of these nucleotide bases determines both the folded conformation and the biological function of RNA. It recently has been established that disparately related functional classes of evolved RNA possess similar base composition biases despite a lack of sequence similarity, folded structure, or metabolic function. We h...