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Biomedical subjects

R Staden

Publications and source records attributed to R Staden.

At least 37 records · Page 2Linked to original sources
PubMed1993

Polar zippers.

BACKGROUND: Certain proteins are known to form leucine zippers - alpha-helical coiled-coils in which the non-polar side chains of two leucine-rich helices intermesh. We recently presented the first evidence for a polar zipper, formed by the carboxy-terminal peptides of the eight subunits of Ascaris haemoglobin. The evidence was based on the presence of pairs of acidic residues alternating with pairs of basic residues ( + + - - ) in an amino-acid sequence that has since been shown to be incomplete. The complete sequence, derived from the haemoglobin's cDNA, now shows a self-complementary polar sequence extending along the entire length of its 24-residue carboxy-terminal peptide. RESULTS: From the complete sequence, it is clear that the eight identical subunits of the haemoglobin could be held together by an eight-stranded antiparallel beta barrel made up of the carboxy-terminal 24 residues of each of the subunits, such that each strand forms 10 salt bridges with each of its neighbours. A computer search of the protein database revealed similar, but shorter, + + - - repeats in several other proteins. It also revealed long repeats of alternating arginine and aspartate residues, and long stretches of only glutamines, or only serines, suggestive of several other kinds of polar zippers. CONCLUSION: Several proteins have amino-acid sequences that suggest the formation of polar zippers made of beta strands. These could form antiparallel pleated sheets linked together by hydrogen bonds between polar side chains both above and below the plane of the sheets. Polar zippers may be important in welding together oligomeric proteins which have subunits lacking the extensive complementary surfaces necessary for stability, or in promoting the association of functionally complementary proteins.

Journal Article↗
PubMed1992

The C. elegans genome sequencing project: a beginning.

The long-term goal of this project is the elucidation of the complete sequence of the Caenorhabditis elegans genome. During the first year methods have been developed and a strategy implemented that is amenable to large-scale sequencing. The three cosmids sequenced in this initial phase are surprisingly rich in genes, many of which have mammalian homologues.

Animals↗
PubMed1992

Indexing the sequence libraries: software providing a common indexing system for all the standard sequence libraries.

We describe a set of programs for creating and using indexes for the distributed forms of the major sequence libraries. The indexes conform to the specification of those distributed on cd-rom by the EMBL sequence library. The programs create entry name, accession number, author and freetext indexes and a brief directory index. If a suitable application program is given an entry name or accession number these indexes allow rapid retrieval of sequences or annotation. Similarly the author and freetext indexes provide the data for extremely fast searching on author names and "keywords". The indexing programs can create indexes for EMBL, Swiss-Prot, GenBANK, PIR and NRL3d libraries. We also describe the organisation and use of the different sequence libraries and their index files.

Abstracting and Indexing↗
PubMed1992

A standard file format for data from DNA sequencing instruments.

There are now a number of machines for determining DNA sequences. These devices are currently of two types: those such as the Applied Biosystems 373A and the Pharmacia A.L.F. which interpret the sequences of samples as they run on gels within the machine, and those, such as the Bio-Rad and Amersham readers that scan and analyse conventional autoradiographs. Both types of machine can produce their data in the form of traces which represent the band intensity of each of the four base types at each position in the sequence. At present all the machines write files in different formats. We describe a machine independent format for storing data derived from automatic sequencing machines. Files in this format can store the derived sequence, the traces and a set of confidence measures for each base. We have adopted the format as the standard for our sequence handling software.

Databases, Factual↗
PubMed1991

A sequence assembly and editing program for efficient management of large projects.

We describe a sequence assembly and editing program for managing large and small projects. It is being used to sequence complete cosmids and has substantially reduced the time taken to process the data. In addition to handling conventionally derived sequences it can use data obtained from Applied Biosystems,Inc. 373A and Pharmacia A.L.F. fluorescent sequencing machines. Readings are assembled automatically. All editing is performed using a mouse operated contig editor that displays aligned sequences and their traces together on the screen. The editor, which can be used on single contigs or for joining contigs, permits rapid movement along the aligned sequences. Insertions, deletions and replacements can be made in individual aligned readings and global changes can be made by editing the consensus. All changes are recorded. A click on a mouse button will display the traces covering the current cursor position, hence allowing quick resolution of problems. Another function automatically moves the cursor to the next unresolved character. The editor also provides facilities for annotating the sequences. Typical annotations include flagging the positions of primers used for walking, or for marking sites, such as compressions, that have caused problems during sequencing. Graphical displays aid the assessment of progress.

Base Sequence↗
PubMed1991

Screening protein and nucleic acid sequences against libraries of patterns.

We describe programs that can screen nucleic acid and protein sequences against libraries of motifs and patterns. Such comparisons are likely to play an important role in interpreting the function of sequences determined during large scale sequencing projects. In addition we report programs for converting the Prosite protein motif library into a form that is compatible with our searching programs. The programs work on VAX and SUN computers.

Amino Acid Sequence↗
PubMed1990

An improved sequence handling package that runs on the Apple Macintosh.

We report improvements to our sequence analysis package and adaptation to run on the Apple Macintosh range of machines. The 'standard' version of the programs, which run on a VAX, has been given a new user interface that makes the programs very much easier to work with and has facilitated the move to the Macintosh. The reorganization of the code should simplify moves to other systems that offer WIMP user interfaces. In addition to a large number of small but useful extra features, some important new analytical functions have been devised. These include sequence and contig editors; optimal alignment and comparison methods; and a new method for comparing the observed and expected frequencies of selected oligonucleotides.

Base Sequence↗
PubMed1989

Methods for calculating the probabilities of finding patterns in sequences.

This paper describes the use of probability-generating functions for calculating the probabilities of finding motifs in nucleic acid and protein sequences. Equations and algorithms are given for calculating the probabilities associated with nine different ways of defining motifs. Comparisons are made with searches of random sequences. A higher level structure--the pattern--is defined as a list of motifs. A pattern also specifies the permitted ranges of spacing allowed between its constituent motifs. Equations for calculating the expected numbers of matches to patterns are given.

Algorithms↗
PubMed1989

Methods for discovering novel motifs in nucleic acid sequences.

We describe a computer tool to aid the discovery of new motifs in nucleic acid sequences. A typical use would be to analyse a set of upstream regions from a family of related genes in order to find possible control sequences. The heart of the method is the creation of dictionaries of related subsequences. These dictionaries can then be analysed to look for the commonest or best-defined subsequences, those that occur in the highest number of different sequences, or for those in equivalent positions within the family. We show the application of the method to a set of E. coli promoter sequences.

Base Sequence↗
PubMed1989

Deviations from expected frequencies of CpG dinucleotides in herpesvirus DNAs may be diagnostic of differences in the states of their latent genomes.

The DNA sequences of genomes from G + C-rich and A + T-rich lymphotropic herpesviruses [i.e. gammaherpesviruses; Epstein-Barr virus and herpesvirus saimiri (HVS)] are deficient in CpG dinucleotides and contain an excess of TpG and CpA dinucleotides relative to frequencies predicted from their mononucleotide compositions. In contrast, for sequences from genomes of G + C-rich and A + T-rich neurotropic herpesviruses (i.e. alphaherpesviruses; herpes simplex virus and varicellazoster virus) and human cytomegalovirus (HCMV; a betaherpesvirus) the mean observed frequencies of these dinucleotides are close to those expected from their mononucleotide compositions. Comparisons between DNA sequences that encode proteins conserved in all these viruses also show that sequences of these lymphotropic viruses are CpG-deficient whereas the homologous genes from the neurotropic viruses and the HCMV are not. Analyses of local variations in dinucleotide frequencies reveal some occurrences of clustered CpG dinucleotides in generally deficient genomes (e.g. upstream of the thymidylate synthase gene of HVS) and locally CpG-deficient regions within some generally non-deficient genomes (e.g. the major immediate early genes of human, simian and murine CMVs). A relative deficiency in CpG and an excess of TpG and CpA dinucleotides is a diagnostic feature of higher eukaryotic DNA sequences that have been subjected to methylation of cytosine residues in CpG doublets with the resulting increase in mutations to give TpG (and thereby its complement, CpA). The available evidence implicates the latent genome as the site of methylation of these herpesviruses. We conclude that in the neurotropic herpesviruses the normal latent precursors to infectious progeny are not methylated whereas there is local methylation of the immediate early locus in the latent genomes of CMVs, and the latent genomes of these lymphotropic herpesviruses are extensively methylated.

Base Sequence↗