A recent article on the IMPALA algorithm by Schäffer et al. (1999) gives the misleading impression that the E-values returned by the MAST algorithm (Bailey and Gribskov, 1998) are unreliable. This erroneous conclusion was reached due to an inappropriate protocol in the experiment involving MAST in the IMPALA article. We have tested MAST using a redesigned protocol that causes MAST to behave as ...

A simple algorithm is presented for the graphic display of nucleic acid secondary structure. Examples of secondary structure displays are given for tRNA, 5S RNA and part of the 16S RNA. Due to its speed, this algorithm could easily be used in conjunction with secondary structure programs which calculate various alternate structures. INTRODUCTION Ever since the first RNA was sequenced, considera...

With an analysis of the structural constraints of the anticodon-codon interaction within the decoding center of the ribosome, we show that the extent of degeneracy at the third position of the anticodon is determined by the level of stability of the base pair at the second position.

Background In stabilization of the G-quadruplex, formation of a Hoogsteen base-pair between the guanine (G) bases is essential. However, the contribution of each Hoogsteen base-pair at different positions to whole stability of the G-quadruplex has not been known. In this study, the effect of a deficiency of the Hoogsteen type hydrogen bond in the G-quadruplex stability was investigated. Spectra...

Functionalisation of quinoline N-oxide was investigated using phophazene base as a catalyst; alkynylation and heteroarylation at 2-position were successfully achieved via nucleophilic addition-elimination process.

I have designed, built, and evaluated a passive radiolocation system that uses only signals of opportunity, that is, signals that exist for purposes other than radiolocation. The system estimates the relative position vector between a base station, which is a navigation receiver at a known location, and a rover, which is like the base station but free to move about. The relative position vector...

The expression of Lewis fucosyltransferase (FT) mRNA was examined in gastric mucosa from two Lewis-positive [Le(+)] and two Lewis-negative [Le(-)] individuals. Northern blot analysis demonstrated that levels of mRNA were similar in both Le(+) and Le(-) gastric mucosa. We isolated the protein-coding region of the Lewis FT cDNA from Le(+) and Le(-) gastric mucosa by polymerase chain reaction (PCR...

Many future applications of robotic systems will require manipulators to operate from moving vehicles. Such vehicles will be compliant in comparison to the rigid bases on which most manipulators are mounted today. Base compliance can seriously degrade system performance. Statically base compliance may lead to error in the position of the end effector, and dynamically base compliance may interac...

Nucleotides in tRNAs that are conserved among isoacceptors are typically considered as candidates for tRNA synthetase recognition, with less importance attached to non-conserved nucleotides. Although the anticodon is an important contributor to the identity of methionine tRNAs, the class I methionine tRNA synthetase aminoacylates microhelices with high specificity. The microhelix substrates are...

The synthesis of the 2'-deoxyadenosine analogues 1b, 2b, and 3c modified at the 7- and/or 2-position is described. The effect of 7-chloro and 2-methylthio groups on the duplex stability is evaluated. For that, the nucleosides 1b, 2b, and 3c were converted to the corresponding phosphoramidites 15, 19, and 22, which were employed in the solid-phase oligonucleotide synthesis. In oligonucleotide du...