Jean Hani

Overview of the yeast genome.

Nature 387 (Suppl.) 9 (1997) The display for chromosome 1 was incorrect as published owing to an error in the production process. The correct figure is shown here.

Erratum: Overview of the yeast genome

Nature 387 (Suppl.) 9 (1997) The display for chromosome 1 was incorrect as published owing to an error in the production process. The correct figure is shown here.

Functional and structural genomics using PEDANT

MOTIVATION Enormous demand for fast and accurate analysis of biological sequences is fuelled by the pace of genome analysis efforts. There is also an acute need in reliable up-to-date genomic databases integrating both functional and structural information. Here we describe the current status of the PEDANT software system for high-throughput analysis of large biological sequence sets and the genome analysis server associated with it. RESULTS The principal features of PEDANT are: (i) completely automatic processing of data using a wide range of bioinformatics methods, (ii) manual refinement of annotation, (iii) automatic and manual assignment of gene products to a number of functional and structural categories, (iv) extensive hyperlinked protein reports, and (v) advanced DNA and protein viewers. The system is easily extensible and allows to include custom methods, databases, and categories with minimal or no programming effort. PEDANT is actively used as a collaborative environment to support several on-going genome sequencing projects. The main purpose of the PEDANT genome database is to quickly disseminate well-organized information on completely sequenced and unfinished genomes. It currently includes 80 genomic sequences and in many cases serves as the only source of exhaustive information on a given genome. The database also acts as a vehicle for a number of research projects in bioinformatics. Using SQL queries, it is possible to correlate a large variety of pre-computed properties of gene products encoded in complete genomes with each other and compare them with data sets of special scientific interest. In particular, the availability of structural predictions for over 300 000 genomic proteins makes PEDANT the most extensive structural genomics resource available on the web.

MIPS: A database for protein sequences and complete genomes

The MIPS group [Munich Information Center for Protein Sequences of the German National Center for Environment and Health (GSF)] at the Max-Planck-Institute for Biochemistry, Martinsried near Munich, Germany, is involved in a number of data collection activities, including a comprehensive database of the yeast genome, a database reflecting the progress in sequencing the Arabidopsis thaliana genome, the systematic analysis of other small genomes and the collection of protein sequence data within the framework of the PIR-International Protein Sequence Database (described elsewhere in this volume). Through its WWW server (http://www.mips.biochem.mpg.de ) MIPS provides access to a variety of generic databases, including a database of protein families as well as automatically generated data by the systematic application of sequence analysis algorithms. The yeast genome sequence and its related information was also compiled on CD-ROM to provide dynamic interactive access to the 16 chromosomes of the first eukaryotic genome unraveled.

The Hansenula polymorpha (strain CBS4732) genome sequencing and analysis

The methylotrophic yeast Hansenula polymorpha is a recognised model system for investigation of peroxisomal function, special metabolic pathways like methanol metabolism, of nitrate assimilation or thermostability. Strain RB11, an odc1 derivative of the particular H. polymorpha isolate CBS4732 (synonymous to ATCC34438, NRRL-Y-5445, CCY38-22-2) has been developed as a platform for heterologous gene expression. The scientific and industrial significance of this organism is now being met by the characterisation of its entire genome. The H. polymorpha RB11 genome consists of approximately 9.5 Mb and is organised as six chromosomes ranging in size from 0.9 to 2.2 Mb. Over 90% of the genome was sequenced with concomitant high accuracy and assembled into 48 contigs organised on eight scaffolds (supercontigs). After manual annotation 4767 out of 5933 open reading frames (ORFs) with significant homologies to a non-redundant protein database were predicted. The remaining 1166 ORFs showed no significant similarity to known proteins. The number of ORFs is comparable to that of other sequenced budding yeasts of similar genome size.

The BioRS TM Integration and Retrieval System: An open system for distributed data integration

Summary Modern academic and industrial research in life sciences generates huge amounts of data and information. To extract knowledge from this information space, optimized integration and retrieval software tools are essential. In the last years, a number of academic as well as commercial systems have been developed to solve this problem. However, as scientific projects are distributed at different locations (e.g., subsidiaries of companies, academic partnerships), data exchange and availability must be realized in a way that avoids data replication. In this article, we describe a global solution for integrating distributed information by applying the BioRSTM Integration and Retrieval System and its inter-BioRS communication capability that goes beyond the standard issue of local data integration. Each site integrates and maintains locally generated data using a local copy of the BioRS software. Applying the inter-BioRS communication, all available BioRS instances can communicate with each other realizing a global network of integrated databanks. All databanks integrated in this network can be accessed from any site without any data replication. This open system allows the addition of new information and sites dynamically. However, access privileges for certain databanks can be maintained on a per user and databank level ensuring data security when required.