Formamide has been widely used in urea/polyacrylamide gel to solve the compression problems that are occasionally found during the DNA sequencing of G/C rich regions. In this study, however, 10% formamide was added in annealing solution in stead of adding to the gel. The compressions were unfolded efficiently with a more rapid annealing reaction on ice in the presence of 10% formamide.
DNA* ; Ice ; Sequence Analysis, DNA*

No abstract available.
Base Sequence* ; DNA* ; Internet* ; Sequence Analysis, DNA*

DNA chips are becoming increasingly popular as a convenient way to perform vast amounts of experiments related to genes on a single chip. And the importance of analyzing the data that is provided by such DNA chips is becoming significant. A very important analysis on DNA chip data would be clustering genes to identify gene groups which have similar properties such as cancer. Clustering data for DNA chips usually deal with a large search space and has a very fuzzy characteristic. The Particle Swarm Optimization algorithm which was recently proposed is a very good candidate to solve such problems. In this paper, we propose a clustering mechanism that is based on the Particle Swarm Optimization algorithm. Our experiments show that the PSO-based clustering algorithm developed is efficient in terms of execution time for clustering DNA chip data, and thus be used to extract valuable information such as cancer related genes from DNA chip data with high cluster accuracy and in a timely manner.
Cluster Analysis ; DNA ; Oligonucleotide Array Sequence Analysis

Pattern finding is one of the important tasks in a protein or DNA sequence analysis. Alignment is the widely used technique for finding patterns in sequence analysis. BLAST (Basic Local Alignment Search Tool) is one of the most popularly used tools in bio-informatics to explore available DNA or protein sequence databases. BLAST may generate a huge output for a large sequence data that contains various sequence patterns. However, BLAST does not provide a tool to summarize and analyze the patterns or matched alignments in the BLAST output file. BLAST lacks of general and robust parsing tools to extract the essential information out from its output. This paper presents a pattern summary system which is a powerful and comprehensive tool for discovering pattern structures in huge amount of sequence data in the BLAST. The pattern summary system can identify clusters of patterns, extract the cluster pattern sequences from the subject database of BLAST, and display the clusters graphically to show the distribution of clusters in the subject database.
Computational Biology ; Databases, Protein ; DNA ; Sequence Analysis* ; Sequence Analysis, DNA

No Abstract Available.
DNA* ; Oligonucleotide Array Sequence Analysis*

Nucleotide analysis of restricted fragment DNA extremities at definite cut sizes identified: there were 3 extremities: flat; cross with DNA 5’; cross with DNA 5’. This study presented a method which able to characterize unknown restriction enzymes by analyzing the cutting extremities of restricted fragments. The method is based on Sanger sequencing of DNA around the cut site and non-radioactive chemical. Klenow reaction had two active characters: analyzing DNA 5’3’ and exonucleasa 3’5’, allowing to determine the type of cutting of restrictive enzymes. This results allowed to identify the cut sizes of two new enzymes: for Sml1, the cut sites occurs within the recognition nucleotide sequence; BciVI recognizing a non-palindrome sequence and cuts outside this sequence.
DNA ; Nucleotides ; analysis ; extremities ; Enzymes

We developed a user-friendly, interactive program to simultaneously cluster and visualize omics data, such as DNA and protein array profiles. This program provides diverse algorithms for the hierarchical clustering of two-dimensional data. The clustering results can be interactively visualized and optimized on a heatmap. The present tool does not require any prior knowledge of scripting languages to carry out the data clustering and visualization. Furthermore, the heatmaps allow the selective display of data points satisfying user-defined criteria. For example, a clustered heatmap of experimental values can be differentially visualized based on statistical values, such as p-values. Including diverse menu-based display options, QCanvas provides a convenient graphical user interface for pattern analysis and visualization with high-quality graphics.
DNA ; Genomics ; Protein Array Analysis

Sequence analysis of human mitochondrial DNA(mtDNA) is being used widely to characterize individual identification, particularly when there is insufficient nuclear DNA in samples for typing. Hair shafts, bones, teeth and other samples that are severely decomposed may be subjected to mtDNA analysis. As sample decomposes, however, the possibility of mtDNA to be degraded becomes high and the possibility of spurious results becomes high. In this case mtDNA sequencing results must be carefully analyzed. We got unusual results while typing two human bone samples, which were not compatible with human mtDNA sequence. Bones were about 50 and 35 years old. We report the results with discussions about ancient DNA sequencing.
Adult ; DNA* ; DNA, Mitochondrial* ; Hair ; Humans ; Sequence Analysis ; Sequence Analysis, DNA ; Tooth

Skeleton and teeth are important biological samples. Due to their special structure and strong ability to resist degradation, they are ideal biological materials to retain DNA under natural condition. In many cases, such as historical figure identification, aged skeleton and teeth are usually the only biological samples. However, their DNA is in a state of trace, damage and degradation to different degrees, which requires special experimental treatment to achieve identification. This paper reviews the sample selection, DNA extraction, DNA enrichment and analysis approaches based on relevant research reports in recent years, aiming to promote the further development and improvement of the aged skeleton and teeth identification system.
Humans ; Aged ; Body Remains ; DNA/analysis* ; Tooth ; DNA Fingerprinting ; Sequence Analysis, DNA

No abstract available.
Cloning, Molecular* ; DNA* ; Helicobacter pylori* ; Helicobacter* ; Sequence Analysis, DNA* ; Urease*