Ray Hagstrom

fastDNAml: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood

We have developed a new tool, called fastDNAml, for constructing phylogenetic trees from DNA sequences. The program can be run on a wide variety of computers ranging from Unix workstations to massively parallel systems, and is available from the Ribosomal Database Project (RDP) by anonymous FTP. Our program uses a maximum likelihood approach and is based on version 3.3 of Felsensteins dnaml program. Several enhancements, including algorithmic changes, significantly improve performance and reduce memory usage, making it feasible to construct even very large trees. Trees containing 40-100 taxa have been easily generated, and phylogenetic estimates are possible even when hundreds of sequences exist. We are currently using the tool to construct a phylogenetic tree based on 473 small subunit rRNA sequences from prokaryotes.

Maximum likelihood genetic sequence reconstruction from oligo content

One promising technique for determining long genetic sequences is sequencing by oligonucleotide content. This technique involves probing a segment of the unknown multimillion “character” genetic sequence for the presence or absence of known short subsequences. The information obtained from such hybridization experiments may be represented in network form. Network optimization methods may then be applied to identify the most likely forms of the unknown target sequence.

An Integrated Database to Support Research on Escherichia Coli

We have used logic programming to design and implement a prototype database of genomic information for the model bacterial organism Escherichia coli. This report presents the fundamental database primitives that can be used to access and manipulate data relating to the E. coli genome. The present system, combined with a tutorial manual, provides immediate access to the integrated knowledge base for E. coli chromosome data. It also serves as the foundation for development of more user-friendly interfaces that have the same retrieval power and high-level tools to analyze complex chromosome organization.

Implementation of a parallel processing system for inference of phylogenetic trees

A parallel processing system for inference of phylogenetic trees is reported. The trees are inferred from DNA sequence data by using a maximum likelihood method based on a stochastic model of the evolutional process. This method gives a good representation of the trees, but the computational cost has hindered the use of this method for inferring trees with more than about 20 species. By a parallel processing method based on a function partitioning approach, the authors reduced the cost significantly and obtained a phylogenetic tree of several hundred species on a massively parallel machine.<<ETX>>

Searching for genomic organizational motifs: Explorations of the Escherichia coli chromosome☆

Understanding the coordinated control of gene expression is a central goal for much of the work in molecular biology. In order to understand how the mechanics of these control systems operate at the genome level, the data for the genetic organization of the model organism in question needs to be accessible. In previous work, we developed an integrated database to support analysis of the Escherichia coli genome. That system provided a pidgin English query facility, rudimentary pattern matching capabilities, and the ability to rapidly extract answers to a wide variety of questions about the organization of the E. coli genome. We have used a parser/grammar approach to identify the chromosomal positions of all of the mapped tRNA genes to be found in the aligned sequence fragments. Also, we have used this integrated data set to explore the global organization of the E. coli chromosome. We have begun to develop regulation classifications based on the arrangements of control features in relation to specific genetic control components. For example, using the individual DNA sequences for 111 known transcriptional promoters as a the starting position for analysis, we have identified the relative positions of potential control sites for 47 different procaryotic transcription factors, sigma factor 70 binding sites, and potential ribosome binding sites that occur within the region −500 to +500 bases upstream or downstream of the anchor position (the first base of the sequence feature). We have defined local descriptions for regulation based on the cross-correlated control features revealed through these analyses.

A technique for achieving portability among multiprocessors: Implementation on the Lemur☆

Abstract We describe here a programming methodology for multiprocessors that leads to well-structured code, ease of debugging, and, most important, portability among multiprocessors offering quire different synchronization primitives. The emphasis in this paper is on the implementation of this methodology for the Lemur, an eight-processor machine built at Argonne National Laboratory. Included are several complete programs illustrating the methodology.

Overview of GRACE-a database system for analysis of multiple genomes

The authors have developed a database system to support analysis of the E. coli genome. That system provides a pidgin-English query facility, rudimentary pattern-matching capabilities, and the ability to rapidly extract answers to a wide variety of questions about the organization of the E. coli genome. To allow the comparative analysis of the genomes from different species, the authors have designed and implemented a new prototype database system, called GRACE. GRACE extends the earlier effort by incorporating a set of curators tools that facilitate the incorporation of physical and genetic data, together with the results of genomic organization analysis, into a common database system. At the present stage of GRACEs development, a curator is expected to have a basic understanding of how data are represented in the Prolog database.<<ETX>>

Comparative analysis of genomic data: A global look at structural and regulatory features

One of the goals of any large scale DNA sequencing project is to understand the molecular details about the metabolic control sites that will be found in the sequence of the chromosome region being studied. In addition, once an interesting observation has been made, questions will quickly arise concerning the distribution of such sites within the genome and how well the same observations hold between related species. This paper will discuss the authors` approach toward building a flexible analysis environment that facilitates the analysis of genomic sequence data. The Integrated Genomic Database (IGD), developed by Ray Hagstrom, Ross Overbeek, Morgan Price and Dave Zawada at the Argonne National Laboratory, organizes genome mapping and sequencing data to provide a global chromosome view for multiple genomes. The authors describe here their use of the IGD system and how they employ it for relational analysis of sequence features that are found distributed throughout the genome under study. The primary goal of this work is to provide a system to support research on the global organization of genomic regulation patterns.

Users guide and tutorial for PC-GenoGraphics: Version 1

PC-GenoGraphics is a visual database/query facility designed for reasoning with genomic data. Data are represented to reflect variously accurate notions of the location of their sites, etc., along the length of the genome. Sequence data are efficiently stored and queried via a rather versatile language so that entire sequences of organisms will be treatable as they emerge. Other classes of information, such as function descriptions, are stored in a relational form, and joint queries relating these to sequence properties are supported. All queries result in visual responses that indicate locations along the genome. The results of queries can themselves be promoted to be queryable objects against which further queries can be launched.

GenoGraphics for OpenWindows{trademark}

GenoGraphics is a generic utility for constructing and querying one-dimensional linear plots. The outgrowth of a request from Dr. Cassandra Smith for a tool to facilitate her genome mapping research. GenoGraphics development has benefited from a continued collaboration with her. Written in Sun Microsystem`s OpenWindows environment and the BTOL toolkit developed at Argonne National Laboratory. GenoGraphics provides an interactive, intuitive, graphical interface. Its features include: viewing multiple maps simultaneously, zooming, and querying by mouse clicking. By expediting plot generation, GenoGraphics gives the scientist more time to analyze data and a novel means for deducing conclusions.