Rapid code phase synchronization is a difficult challenge for direct sequence spread spectrum systems that utilize long spreading codes. Current synchronization techniques have been limited to either exhaustive search over the spreading code time-frequency uncertainty region, or various ad hoc techniques, which work only at high signal to noise ratios. This paper presents an entirely new approach to the code acquisition problem based on the adaptation of convolutional decoding techniques. The method is denoted STARS for state transition assisted receiver/synchronizer. STARS is much faster than the traditional code search process, and can operate at very low signal to noise ratios

We present a new method for the identification of conserved patterns in a set of unaligned related protein sequences. It is able to discover patterns of a quite general form, allowing for both ambiguous positions and for variable length wildcard regions. It allows the user to define a class of patterns (e.g., the degree of ambiguity allowed and the length and number of gaps), and the method is then guaranteed to find the conserved patterns in this class scoring highest according to a significance measure defined. Identified patterns may be refined using one of two new algorithms. We present a new (nonstatistical) significance measure for flexible patterns. The method is shown to recover known motifs for PROSITE families and is also applied to some recently described families from the literature.

The sequence of the PcnB protein of Escherichia coli, a protein required for copy number maintenance of ColE1-related plasmids, was compared with the PIR sequence database. Strong local similarities to the sequence of the E. coli protein tRNA nucleotidyltransferase were found. Since a substrate of the latter protein, tRNA, structurally resembles the RNAs that control ColE1 copy number we believe that we may have identified a region in PcnB that interacts with these RNAs. Consistent with this idea is our observation that PcnB is required for the replication of R1, a plasmid whose replication is also regulated by a small RNA.

Molecular biology analyses the molecular basis of living systems. The chemical complexity of biological systems of importance (e.g. enzyme action, organelle assembly, membrane transport, antigen-antibody reactions, cell recognition and many others) is at the extreme end of the range to which many physical methods of analysis can be applied. Developments will follow progress in the physical sciences, which in turn depends extensively on high performance computer modelling and investigation. The author discusses two major areas of computer applications in molecular biology, which exploit massively parallel computing systems

The amino acid sequences of mammalian protein phosphatase 1 and 2A were compared pairwise with every sequence in the National Biomedical Research Foundation protein sequence database using an exhaustive searching programme [Coulson et al., Comp. J. 30 (1987) 420-424]. The N-terminal half of the protein encoded by an open reading frame, orf 221, in bacteriophage lambda (nt 43,224-43,886 in the map of Daniels et al. [in Hendrix et al. (Eds.), Lambda II. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 1983, pp. 519-676] shows 35% identity to either protein phosphatase 1 or 2A in this region. If conservative replacements are included the overall homology rises to 49%. A gene in phi 80 also shows 35% identity with the mammalian protein phosphatases. The results indicate that orf 221 of phage lambda and the homologous phi 80 gene may encode protein phosphatases. The possible roles of protein phosphorylation in the propagation of bacteriophage are discussed.

Sequence analysis of protein and nucleic acid databases by exhaustive string-matching algorithms is effectively implemented on large processor-array machines, such as the I.C.L. DAP. An improved method of assessing the significance of the best alignments for proteins is described. Examples involving the cystic fibrosis antigen and Drosophila vitellogenins illustrate the usefulness of this approach.

Programs have been written to apply parallel processing algorithms to the main methods of DNA sequence analysis. These programs allow the largest of currently interesting problems to be handled on a medium-sized computer system. The abundance of information otherwise not readily available has suggested new methods for the detection of homology and order in sequences.

AT the high cell densities normally used in E.coli matings (about 108 cells per ml) individual cells undergo frequent and repeated collisions, and should therefore have multiple opportunities for pairing1–3. A mating pair of cells, once formed, will similarly continue to collide almost as frequently with other cells. It is not known whether these secondary collisions affect either the speed or extent of DNA transfer, since the true properties of a mating pair of cells formed with little likelihood of further collisions have not been studied. Pairs formed at low cell concentrations, however, should be suitable for such studies; indeed, they could be regarded as paradigms of simple cell–cell interactions. We show here that at low densities pair formation is much more efficient than at high densities, and also that motility decreases this efficiency once cells have collided.

The thermal decomposition of both cis-and trans-2-methoxy-4-methyl-3,4-dihydro-2H-pyran has been investigated in the gas phase from 287 to 345°. In this temperature range both isomers decomposed to give crotonaldehyde and methyl vinyl ether by a homogeneous process that obeyed first-order kinetics. The data for the trans-isomer yileded the Arrhenius equation (i). Similarly the cis-isomer gave equation (ii). These results log k1/s–1= 14·246 ± 0·106 –(201·46 + 1·20 kJ mol–1)RTIn 10 (i), log k2/s–1= 13·958 ± 0·062 –(196·00 ± 0·70 kJ mol–1)RTIn 10 (ii) are discussed in terms of a unimolecular decomposition occurring by a concerted mechanism.

Zwischen 287 und 345°C werden beide Isomere zu Crotonaldehyd und Methylvinyl‐ äther zersetzt.