Biomedical subjects

R Giegerich

Publications and source records attributed to R Giegerich.

9 recordsLinked to original sources

PubMed2001

REPuter: the manifold applications of repeat analysis on a genomic scale.

The repetitive structure of genomic DNA holds many secrets to be discovered. A systematic study of repetitive DNA on a genomic or inter-genomic scale requires extensive algorithmic support. The REPuter program described herein was designed to serve as a fundamental tool in such studies. Efficient and complete detection of various types of repeats is provided together with an evaluation of significance and interactive visualization. This article circumscribes the wide scope of repeat analysis using applications in five different areas of sequence analysis: checking fragment assemblies, searching for low copy repeats, finding unique sequences, comparing gene structures and mapping of cDNA/EST sequences.

Algorithms↗

PubMed2001

Minimum conflict: a divide-and-conquer approach to phylogeny estimation.

MOTIVATION: Fast and reliable phylogeny estimation is rapidly gaining importance as more and more genomic sequence information is becoming available, and the study of the evolution of genes and genomes accelerates our understanding in biology and medicine alike. Branch attraction phenomena due to unequal amounts of evolutionary change in different parts of the phylogeny are one major problem for current methods, placing the species that evolved fast in one part of the phylogenetic tree, and the species that evolved slowly in the other. RESULTS: We describe a way to avoid the artifactual attraction of species that evolved slowly, by detecting shared old character states using a calibrated comparison with an outgroup. The corresponding focus on shared novel character states yields a fast and transparent phylogeny estimation algorithm, by application of the divide-and-conquer principle, and heuristic search: shared novelties give evidence of the exclusive common heritage (monophyly) of a subset of the species. They indicate conflict in a split of all species considered, if the split tears them apart. Only the split at the root of the phylogenetic tree cannot have such conflict. Therefore, we can work top-down, from the root to the leaves, by heuristically searching for a minimum-conflict split, and tackling the resulting two subsets in the same way. The algorithm, called "minimum conflict phylogeny estimation" (MCOPE), has been validated successfully using both natural and artificial data. In particular, we reanalyze published trees, yielding more plausible phylogenies, and we analyze small "undisputed" trees on the basis of alignments considering structural homology. AVAILABILITY: MCOPEis available via http://bibiserv.techfak.uni-bielefeld.de/mcope/. CONTACT: fuellen@alum.mit.edu

Algorithms↗

PubMed2000

A systematic approach to dynamic programming in bioinformatics.

MOTIVATION: Dynamic programming is probably the most popular programming method in bioinformatics. Sequence comparison, gene recognition, RNA structure prediction and hundreds of other problems are solved by ever new variants of dynamic programming. Currently, the development of a successful dynamic programming algorithm is a matter of experience, talent and luck. The typical matrix recurrence relations that make up a dynamic programming algorithm are intricate to construct, and difficult to implement reliably. No general problem independent guidance is available. RESULTS: This article introduces a systematic method for constructing dynamic programming solutions to problems in biosequence analysis. By a conceptual splitting of the algorithm into a recognition and an evaluation phase, algorithm development is simplified considerably, and correct recurrences can be derived systematically. Without additional effort, the method produces an early, executable prototype expressed in a functional programming language. The method is quite generally applicable, and, while programming effort decreases, no overhead in terms of ultimate program efficiency is incurred.

Algorithms↗

PubMed2000

Computation and visualization of degenerate repeats in complete genomes.

Algorithms↗

PubMed1999

RNA movies: visualizing RNA secondary structure spaces.

MOTIVATION: RNA Movies is a system for the visualization of RNA secondary structure spaces. Its input is a script consisting of primary and secondary structure information. From this script, the system fully automatically generates animated graphical structure representations. In this way, it creates the impression of an RNA molecule exploring its own two-dimensional structure space. RESULTS: RNA Movies has been used to generate animations of a switching structure in the spliced leader RNA of Leptomonas collosoma and sequential foldings of potato spindle tuber viroid transcripts. AVAILABILITY: Demonstrations of the animations mentioned in this paper can be viewed on our Bioinformatics web server under the following address: http://BiBiServ.TechFak.Uni-Bielefeld. DE/rnamovies/. The RNA Movies software is available upon request from the authors.

Algorithms↗

PubMed1999

Prediction and visualization of structural switches in RNA.

There are various cases where the biological function of an RNA molecule involves a reversible change of conformation. paRNAss is a software approach to the prediction of such structural switching in RNA. It is based on three hypotheses about the secondary structure space of a switching RNA molecule, which can be evaluated by RNA folding and structure comparison. In the positive case, the predicted structures must be verified experimentally. Additionally, we give an animated visualization of an energetically favourable transition between the predicted structures. paRNAss is available via the Bielefeld Bioinformatics Server. This paper explains the underlying model and shows that the approach performs well in a variety of applications.

Base Sequence↗

PubMed1997

RIFLE: rapid identification of microorganisms by fragment length evaluation.

Biological macromolecules represent a valuable source of information for the identification and phylogenetic classification of microorganisms. One of the most commonly used macromolecules for this task is the 16S rDNA. The WWW-based RIFLE system presented here supports large-scale identification tasks by comparing 16S rDNA restriction patterns to a database of restriction patterns derived from sequence databases. Computing efficiency and robustness against experimental errors are gained by employing a new distance measure for restriction patterns, the fragment length distance. Results from the application of the system to the identification of uncultured microorganisms associated with the seagrass halophila stipulacea show the reliability of the method.

Algorithms↗

PubMed1996

GeneFisher--software support for the detection of postulated genes.

When a family of genes from closely related organisms is known, there is a certain change to extract the corresponding gene from the genome of another related organism. This can be done by polymerase chain reaction, provided that a pair of suitable primers can be designed. In contrast to primer design for a single, known target sequence, systematic primer design for an unknown target given a group of homologues can by no means be done manually. GeneFisher is a software tool which automates this task, and takes special care to make the impact of the manifold design parameters transparent to the user.

Algorithms↗

PubMed1996

Distance education through the Internet: the GNA-VSNS biocomputing course.

A prototype course on biocomputing was delivered via international computer networks in early summer 1995. The course lasted 11 weeks, and was offered free of charge. It was organized by the BioComputing Division of the Virtual School of Natural Sciences, which is a member school of the Globewide Network Academy. It brought together 34 students and 7 instructors from all over the world, and covered the basics of sequence analysis. Five authors from Germany and USA prepared a hypertext book which was discussed in weekly study sessions that took place in a virtual classroom at the BioMOO electronic conferencing system. The course aimed at students with backgrounds in molecular biology, biomedicine or computer science, complementing and extending their skills with an interdisciplinary curriculum. Special emphasis was placed on the use of Internet resources, and the development of new teaching tools. The hypertext book includes direct links to sequence analysis and databank search services on the Internet. A tool for the interactive visualization of unit-cost pairwise sequence alignment was developed for the course. All course material will stay accessible at the World Wide Web address (Uniform Resource Locator) http://+www.techfak.uni-bielefeld.de/bcd/welcome .html. This paper describes the aims and organization of the course, and gives a preliminary account of this novel experience in distance education.

Computational Biology↗