Algorithms and software for support of gene identification experiments

MOTIVATION: Gene annotation is the final goal of gene prediction algorithms. However, these algorithms frequently make mistakes and therefore the use of gene predictions for sequence annotation is hardly possible. As a result, biologists are forced to conduct time-consuming gene identification experiments by designing appropriate PCR primers to test cDNA libraries or applying RT-PCR, exon trapping/amplification, or other techniques. This process frequently amounts to 'guessing' PCR primers on top of unreliable gene predictions and frequently leads to wasting of experimental efforts. RESULTS: The present paper proposes a simple and reliable algorithm for experimental gene identification which bypasses the unreliable gene prediction step. Studies of the performance of the algorithm on a sample of human genes indicate that an experimental protocol based on the algorithm's predictions achieves an accurate gene identification with relatively few PCR primers. Predictions of PCR primers may be used for exon amplification in preliminary mutation analysis during an attempt to identify a gene responsible for a disease. We propose a simple approach to find a short region from a genomic sequence that with high probability overlaps with some exon of the gene. The algorithm is enhanced to find one or more segments that are probably contained in the translated region of the gene and can be used as PCR primers to select appropriate clones in cDNA libraries by selective amplification. The algorithm is further extended to locate a set of PCR primers that uniformly cover all translated regions and can be used for RT-PCR and further sequencing of (unknown) mRNA.      

Recent evolutionary history of American Onchocerca volvulus, based on analysis of a tandemly repeated DNA sequence family

Polymerase chain reaction (PCR) products were characterized for a repeated sequence family (designated "O-150") of the human filarial parasite Onchocerca volvulus. In phylogenetic inferences, the O-150 sequences clustered into closely related groups, suggesting that concerted evolution maintains sequence homology in this family. Using a novel mathematical model based on a nested application of an analysis of variance, we demonstrated that African rainforest and savannah strain parasite populations are significantly different. In contrast, parasites collected in the New World are indistinguishable from African savannah strains of O. volvulus. This finding supports the hypothesis that onchocerciasis was recently introduced into the New World, possibly as a result of the slave trade.      

Rapid in vitro sulfoxidation of chlorpromazine by human blood: inhibition by an endogenous plasma protein factor.

Sulfoxidation of chlorpromazine is a major metabolic pathway in humans and is clinically significant insofar as chlorpromazine-sulfoxide is thought to be pharmacologically inactive. Sulfoxidizing capacities of hepatic and extrahepatic tissues were examined $\text{in vitro}$. Liver, lung, and gut, but not brain, were found to have differential activities (liver>lung>gut) which were NADPH dependent and had characteristics of enzymatic reactions. NADPH independent sulfoxidation of chlorpromazine is seen in the presence of whole blood. This reaction reaches completion in less than 5 sec. and is considerably more active than that seen with other tissues; the total sulfoxidizing capacity of whole blood can be attributed to hemoglobin.Plasma contains a protein-like factor that actively inhibits blood-catalyzed chlorpromazine sulfoxidation. This factor has a molecular weight of 72,000±6000 daltons. The possible roles of this protein in regulating phenothiazine metabolism are discussed.