PABAP (Palindrome Analysis by BLAST Program) is an analysis system that identifies palindromic sequences from a large genome sequence up to several megabases long. It uses NCBI BLAST as a searching engine, and data processing such as alignment filtration and detection of inverted repeats which satisfy user- defined parameters is performed by manipulating data after populating into a MySQL database. PABAP outperforms publicly available palindrome search program in that it can detect large palindrome with internal spacer at a faster speed from bacterial genomes. It is a standalone application and is freely available for noncommercial users. AVAILABILITY: This application was implemented with free software (Perl, Apache, MySQL, and NCBI BLAST) and is freely available to noncommercial users upon request. Analysis of user data can be carried out directly at http://chimp.kribb.re.kr/~javamint/palindrome.
APACHE ; Filtration ; Genome* ; Genome, Bacterial

An increasing number of primate genomes are being sequenced. A direct comparison of repeat elements in human genes and their corresponding chimpanzee orthologs will not only give information on their evolution, but also shed light on the major evolutionary events that shaped our species. We have developed REPEATOME to enable visualization and subsequent comparisons of human and chimpanzee repeat elements. REPEATOME (http://www.repeatome.org/) provides easy access to a complete repeat element map of the human genome, as well as repeat element-associated information. It provides a convenient and effective way to access the repeat elements within or spanning the functional regions in human and chimpanzee genome sequences. REPEATOME includes information to compare repeat elements and gene structures of human genes and their counterparts in chimpanzee. This database can be accessed using comparative search options such as intersection, union, and difference to find lineage-specific or common repeat elements. REPEATOME allows researchers to perform visualization and comparative analysis of repeat elements in human and chimpanzee.
Genome ; Genome, Human ; Humans* ; Pan troglodytes* ; Primates

Genome-wide association (GWA) studies are the method of choice for discovering loci associated with common diseases. More than a thousand GWA studies have reported successful identification of statistically significant association signals in human genomes for a variety of complex diseases. In this review, I discuss some of the issues related to the future of GWA studies and their biomedical applications.
Genome, Human ; Genome-Wide Association Study ; Humans

Nuclear mitochondrial DNA segment (Numt) insertion describes a well-known phenomenon of mitochondrial DNA transfer into a eukaryotic nuclear genome. However, it has not been well understood, especially in plants. Numt insertion patterns vary from species to species in different kingdoms. In this study, the patterns were surveyed in nine plant species, and we found some tip-offs. First, when the mitochondrial genome size is relatively large, the portion of the longer Numt is also larger than the short one. Second, the whole genome duplication event increases the ratio of the shorter Numt portion in the size distribution. Third, Numt insertions are enriched in exon regions. This analysis may be helpful for understanding plant evolution.
DNA, Mitochondrial* ; Exons ; Genome ; Genome, Mitochondrial ; Plants*

No abstract available.
Genome, Human* ; Human Genome Project* ; Humans ; Humans*

No abstract available.
Genome* ; Humans* ; Pan troglodytes*

Recent rapid advances in genetic research are ushering us into the genome sequence era, where an individual's genome information is utilized for clinical practice. The most spectacular results of the human genome study have been provided by genome-wide association studies (GWASs). This is a review of the history of GWASs as related to my work. Further efforts are necessary to make full use of its potential power to medicine.
Genetic Research ; Genome ; Genome, Human ; Genome-Wide Association Study ; HapMap Project ; Human Genome Project ; Humans

A few bioinformatics tools have been used to find out conserved regions as probes. We have developed a system based on a heuristic method with web interfaces to find out conserved regions against microbial genomes. The system runs in real time by using relative entropy in limited narrow regions and detecting similar regions between pair regions with local alignment. The system could be useful to find out conserved regions as genome-wide scale.
Computational Biology ; Entropy ; Genome

The excellent achievement of encoding human gene strongly impacted not only to medicine but also pharmacy. Based on knowledge of human genome, one new speciality appears in pharmacy, it is Pharmacogenomics, studies in the effects and side-effects of drugs, and finds out the new produce methods based on gene. The main technologies in Pharmacogenomics are molecular biotechnology, gene technology, molecular enzyme, especially SNPs technique. Pharmacogenomics gained many important achievements in improving of drug effects, especially drugs for treating of neuropathy and cardiovascular diseases, in studying drug resistance of bacteria, virus. Targets are 'personalized pharmacy' to produce, provide for each patient drug that appropriate to his genome in order to optimize drug effects, minimally or completely reduce side-effects
Pharmacogenetics ; Genome ; Pharmaceutical Preparations ;

In June 26, 2000, doctor Collins and Venter released the results of research of human genome. As the results, the human genome has 3.12 billion nucleotides (nu) of which the sequence of 97% nucleotides were identified. There were 60.000 -100.000 genes found among 3.12 billion nucleotides. The human genome is identical from one to another (99.9%) although there is a difference of races, skin color. Genome is a foundation of the biology and considered as an electronic central nerve of the cells. The basic techniques for research on genes comprise the DNA recombination, chemical analysis (MAXAM GILBERT) and method SANGER.
Genome, Human ; Biology ; DNA