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H W Mewes

Publications and source records attributed to H W Mewes.

51 records · Page 3Linked to original sources
PubMed1996

Life with 6000 genes.

The genome of the yeast Saccharomyces cerevisiae has been completely sequenced through a worldwide collaboration. The sequence of 12,068 kilobases defines 5885 potential protein-encoding genes, approximately 140 genes specifying ribosomal RNA, 40 genes for small nuclear RNA molecules, and 275 transfer RNA genes. In addition, the complete sequence provides information about the higher order organization of yeast's 16 chromosomes and allows some insight into their evolutionary history. The genome shows a considerable amount of apparent genetic redundancy, and one of the major problems to be tackled during the next stage of the yeast genome project is to elucidate the biological functions of all of these genes.

Amino Acid Sequence↗
PubMed1996

The PIR-International Protein Sequence Database.

From its origin the Protein Sequence Database has been designed to support research and has focused on comprehensive coverage, quality control and organization of the data in accordance with biological principles. Since 1988 the database has been maintained collaboratively within the framework of PIR-International, an association of macromolecular sequence data collection centers dedicated to fostering international cooperation as an essential element in the development of scientific databases. The database is widely distributed and is available on the World Wide Web, via ftp, email server, on CD-ROM and magnetic media. It is widely redistributed and incorporated into many other protein sequence data compilations, including SWISS-PROT and the Entrez system of the NCBI.

Amino Acid Sequence↗
PubMed1996

A top-down approach to whole genome visualization.

The investigation of large DNA contigs like complete chromosomes or genomes requires novel methods of data visualization. The complex information contained in a genome, particularly the relation of its individual genetic elements, needs to be accessible in a comprehensive, intelligent and intelligible manner. The yeast genome is expected to contain more than 6,000 Open Reading Frames (ORFs). As yet, the function of many of these ORFs has not been characterized satisfactorily. Also, many ORFs are found to have redundant copies elsewhere in the genome that originated from common ancestors. Other genetic elements (e.g. Tss, delta-elements, t-RNAs) are present in multiple copies. To visualize these relationships, a top-down "genome browser" is introduced that enables inspection of genomic data at different levels of abstraction (e.g. chromosomes, coding/non-coding regions, high/low levels of similarity). This novel tool is a key component for the integrated services approach to biological sequence data management (Heumann et al. 1995) and is accessible through the world wide web (WWW). This work demonstrates how the genome browser visualizes the results of an all-against-all comparison of the elements in the yeast genome as a graph. Interactive navigational queries across yeast chromosomes along the lines of sequence similarity open versatile options for the detailed investigation of genome properties. For sequence comparison the hashed position tree HPT (Mewes & Heumann 1995) is applied. Sequence similarity relationships are represented using the genome similarity graph (GSG) (Heumann & Mewes 1996c).

Chromosomes, Fungal↗
PubMed1994

Complete DNA sequence of yeast chromosome II.

In the framework of the EU genome-sequencing programmes, the complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome II (807 188 bp) has been determined. At present, this is the largest eukaryotic chromosome entirely sequenced. A total of 410 open reading frames (ORFs) were identified, covering 72% of the sequence. Similarity searches revealed that 124 ORFs (30%) correspond to genes of known function, 51 ORFs (12.5%) appear to be homologues of genes whose functions are known, 52 others (12.5%) have homologues the functions of which are not well defined and another 33 of the novel putative genes (8%) exhibit a degree of similarity which is insufficient to confidently assign function. Of the genes on chromosome II, 37-45% are thus of unpredicted function. Among the novel putative genes, we found several that are related to genes that perform differentiated functions in multicellular organisms of are involved in malignancy. In addition to a compact arrangement of potential protein coding sequences, the analysis of this chromosome confirmed general chromosome patterns but also revealed particular novel features of chromosomal organization. Alternating regional variations in average base composition correlate with variations in local gene density along chromosome II, as observed in chromosomes XI and III. We propose that functional ARS elements are preferably located in the AT-rich regions that have a spacing of approximately 110 kb. Similarly, the 13 tRNA genes and the three Ty elements of chromosome II are found in AT-rich regions. In chromosome II, the distribution of coding sequences between the two strands is biased, with a ratio of 1.3:1. An interesting aspect regarding the evolution of the eukaryotic genome is the finding that chromosome II has a high degree of internal genetic redundancy, amounting to 16% of the coding capacity.

Base Composition↗
PubMed1994

A new concept of sequence data distribution on wide area networks.

Accepted concepts in distributed applications design have been applied in the development of a network-based system for the synchronization of remote sequence database access sites by an incremental update mechanism. Computer hardware requirements, network bandwidth, and stability considerations make centralized access to essential computerized resources undesirable. A network model has been developed to distribute access over a collection of remotely situated computer centers. The formally independent database-access nodes join to form a heterogeneous, long distance, co-operating network that can compensate for the deficiencies of unstable network links thereby ensuring uninterrupted access to the resource. In order to guarantee consistency among these nodes, several distributed transaction protocols have been investigated; based on these results, a prototype system has been implemented. A layered software architecture makes the distributed transaction protocol transparent to the individual database system and the underlying network. Individual components of this network communicate by means of Remote Procedure Calls (RPCs). A prototype software system operates to synchronize up to data copies of the PIR-International Protein Sequence Database (Barker et al., 1993) at a number of different sites using the public Internet as the transport vehicle.

Computer Communication Networks↗
PubMed1994

The PIR-International Protein Sequence Database.

PIR-International is an association of macromolecular sequence data collection centers dedicated to fostering international cooperation as an essential element in the development of scientific databases. A major objective of PIR-International is to continue the development of the Protein Sequence Database as an essential public resource for protein sequence information. This paper briefly describes the architecture of the Protein Sequence Database and how it and associated data sets are distributed and can be accessed electronically.

Amino Acid Sequence↗
PubMed1993

The PIR-International databases.

PIR-International is an association of macromolecular sequence data collection centers dedicated to fostering international cooperation as an essential element in the development of scientific databases. PIR-International is most noted for the Protein Sequence Database. This database originated in the early 1960's with the pioneering work of the late Margaret Dayhoff as a research tool for the study of protein evolution and intersequence relationships; it is maintained as a scientific resource, organized by biological concepts, using sequence homology as a guiding principle. PIR-International also maintains a number of other genomic, protein sequence, and sequence-related databases. The databases of PIR-International are made widely available. This paper briefly describes the architecture of the Protein Sequence Database, a number of other PIR-International databases, and mechanisms for providing access to and for distribution of these databases.

Amino Acid Sequence↗
PubMed1992

Workshop on two-dimensional gel protein databases.

A workshop on two-dimensional gel electrophoresis (2-DE) protein database, organized by the Committee on Data for Science and Technology (CODATA) of the International Council of Scientific Unions Task Group on Biological Macromolecules, was held at the CODATA Secretariat in Paris on March 9, 1992. Eleven scientists from eight different countries represented various aspects of 2-DE analysis--namely, cellular protein database development and protein microsequencing methodologies. The purpose of the workshop was to explore means of integrating the rapidly expanding body of information on 2-DE resolved proteins from different laboratories. A major proposal emanating from the workshop was the establishment of an intermediary or "relational" 2-DE gel protein database. This intermediary database, which would catalogue pertinent information on 2-DE resolved proteins (experimental source, 2-DE loci, biological information, etc.) could be an adjunct to, and accessed through, the existing international protein sequence databanks. It would function as a pointer for researchers to the individual 2-DE protein databases where primary and more specialized 2-DE data would be housed.

Databases, Factual↗
PubMed1987

A rapid vapor-phase acid (hydrochloric acid and trifluoroacetic acid) hydrolysis of peptide and protein.

A new method for the acid hydrolysis of protein is presented. Peptide bonds are cleaved by the action of an HCl/trifluoroacetic acid (TFA) vapor mixture. Contamination for the hydrolysis mixture is reduced to low levels (1-3 pmol). Recovery of hydrophobic amino acid is improved. Short reaction times are achieved and rapid removal of acids is facilitated. The reaction temperature is 158 degrees C for reaction times of 22.5 and 45 min with 7 M HCl and 10% TFA containing 0.1% phenol.

Amino Acids↗
PubMed1987

A standardized format for sequence data exchange.

At present there is no agreement upon a standard format for the presentation of sequence data; each of the major sequence databases has adopted their own format. As a result, efforts to pool these data and to develop software to manipulate the data have been hampered. A significant amount of software development time must be invested to handle the incompatibilities among these formats before software to solve biologically interesting problems can be implemented. In principle, the development of a standard format by the database distributors would be the best solution. However, because the databases have invested years of effort in the development of procedures specifically tailored to their own format, they are reluctant to change. Insisting that they convert to a new format would place an extreme burden on the already overtaxed resources of these groups. Furthermore, for certain specialized applications it is more efficient to present the data in nonstandard formats. An alternative solution is presented here. Rather than develop a single standard format for all sequence data, a standardized exchange format has been developed. This format was designed to serve as a common interface between the major formats currently in use. Data can be easily converted to and from it without significant loss of information. This alleviates difficulties inherent in dealing with multiple formats while preserving the local formats of the various databases.

Amino Acid Sequence↗