The method we have developed allows the cytoplasm of a single fossil cell to be sufficiently preserved as to be distinguished by fluorescence microscopy. Analysis of fossil DNA involved PCR amplification of the spacer region between rrn5 and trnR genes in the chloroplast genome. The DNA and consensus sequences, obtained from the same PCR amplification fragment, were analysed by BLAST search and...

Consensus sequences are widely used in molecular biology but they have many flaws. As a result, binding sites of proteins and other molecules are missed during studies of genetic sequences and important biological effects cannot be seen. Information theory provides a mathematically robust way to avoid consensus sequences. Instead of using consensus sequences, sequence conservation can be quanti...

We have developed an automated system for management of DNA sequencing projects. The system, named GEL, can handle data from both random sequences and from fragments whose relative positions are known. The system is highly interactive, self-documenting, and forgiving; it is designed for use by computer-naive molecular biologists. An editor designed specifically for sequences allows simple entry...

During the past several years, the use of computer programs in the analysis of protein and DNA sequences has become commonplace. In all but the simplest procedures, the ability to critically review the results obtained with computer methods requires i) a basic knowledge of the algorithms employed (and the assumptions upon which they are based), ii) an awareness of the capabilities and limitatio...

The intrinsic redundancy of genetic information makes searching for patterns in biological sequences a difficult task. We have designed an interactive self-documenting computer program called QUEST that allows rapid searching of large DNA and protein data banks for highly redundant consensus sequences or character patterns. QUEST uses a concise language for specifying character patterns contain...

We study diierent genetic algorithm operatorsfor one permutationproblem associated with the Human Genome Project|the assembly of DNA sequence fragments from a parent clone whose sequence is unknown into a consensus sequence corresponding to the parent sequence. The sorted-order representation, which does not require specialized operators, is compared with a more traditional permutation represen...

MOTIVATION Summarizing and displaying the information contained in a set of aligned sequences is an important aid to identifying patterns within the sequences. A variety of forms of consensus sequences have been used previously to provide this information. However, these methods can cause a loss of information or introduce ambiguities into the consensus sequence, and some graphical approaches m...

m a-Crystallins were demonsl:rated recently to be involved fin interaction with a short element of the sense strand of the murine yDE/F-ctystallin genes immediately downstresm of the transcriptional initiation site @OTIS). The aim of the study was to demonstrate a consensus sequence and to test, if the interaction with a-crystallin is dependent on phospholylation. M&&& 3*P-labelled oligonucleot...

MOTIVATION Alternative splicing is currently seen to explain the vast disparity between the number of predicted genes in the human genome and the highly diverse proteome. The mapping of expressed sequences tag (EST) consensus sequences derived from the GeneNest database onto the genome provides an efficient way of predicting exon-intron boundaries, gene structure and alternative splicing events...

This paper describes a new method for determining the consensus sequences that signal the start of translation and the boundaries between exons and introns (donor and acceptor sites) in eukaryotic mRNA. The method takes into account the dependencies between adjacent bases, in contrast to the usual technique of considering each position independently. When coupled with a dynamic program to compu...