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Showing papers on "Munich Information Center for Protein Sequences published in 2005"


Journal ArticleDOI
TL;DR: To develop an integrated cross-species plant genome resource, this work maintains comprehensive databases for model plant genomes, including Arabidopsis (Arabidopsis thaliana), maize (Zea mays), Medicago truncatula, and rice (Oryza sativa).
Abstract: With several plant genomes sequenced, the power of comparative genome analysis can now be applied. However, genome-scale cross-species analyses are limited by the effort for data integration. To develop an integrated cross-species plant genome resource, we maintain comprehensive databases for model plant genomes, including Arabidopsis (Arabidopsis thaliana), maize (Zea mays), Medicago truncatula, and rice (Oryza sativa). Integration of data and resources is emphasized, both in house as well as with external partners and databases. Manual curation and state-of-the-art bioinformatic analysis are combined to achieve quality data. Easy access to the data is provided through Web interfaces and visualization tools, bulk downloads, and Web services for application-level access. This allows a consistent view of the model plant genomes for comparative and evolutionary studies, the transfer of knowledge between species, and the integration with functional genomics data.

21 citations


Proceedings ArticleDOI
09 May 2005
TL;DR: MicrobaseLite as discussed by the authors is a grid-based system for genome comparison and analysis, which uses a scalable computing environment to support computationally intensive microbial genome comparison, employing state-of-the-art technologies of Web services, notification, comparative genomics and parallel computing.
Abstract: Genome comparison and analysis can reveal the structures and junctions of genome sequences of different species. As more genomes are sequenced, genomic data sources are rapidly increasing such that their analysis is beyond the processing capabilities of most research institutes. The grid is a powerful solution to support large-scale genomic data processing and genome analysis. This paper presents the Microbase project that is developing a grid-based system for genome comparison and analysis, and discusses the first implementation of the system (called MicrobaseLite). MicrobaseLite uses a scalable computing environment to support computationally intensive microbial genome comparison and analysis, employing state-of-the-art technologies of Web services, notification, comparative genomics and parallel computing. Microbase will support not only system-defined genome comparison and analysis but also user-defined, remotely conceived genome analysis.

11 citations


Proceedings ArticleDOI
05 Dec 2005
TL;DR: A package of integrated comparative analysis platform (iCAP) for comparing various genomes from sequence level to pathway level and use locally sequenced bacterial species as examples to present some of the discovered features for genome design.
Abstract: Till the end of June 2005, there are totally around 1500 complete and ongoing genome sequencing projects (see the GOLD at http://www.genomesonline.org/) around the world. Near two hundred and fifty bacterial genomes have already been completely sequenced and other seven hundreds more are currently underway. The availability of the tremendous amount of whole genome sequences has no doubt opened up new avenues for genome-wide innovative genome design and efficient synthetic biology research. With such abundant resources, we do indeed need to develop tools for analyzing these sequences and mining the genomic treasures among these species. By analyzing the whole genomes for similarities/differences and structural features, it has become possible to identify new genetic targets and investigate their roles. Our group is interested in studying the architectural structures of the various genomes by many novel methods used to characterize genome structure in natural living cells and investigating their use in genome design and engineering. To aid this kind of comparative genome analysis, we have developed efficient gene identification and functional annotation pipeline and also constructed tools that can plot numerous measures for all positions in a long DNA sequence and do multiple whole genome comparisons. In this report, we would like to present a package of integrated comparative analysis platform (iCAP) for comparing various genomes from sequence level to pathway level and use locally sequenced bacterial species as examples to present some of the discovered features for genome design.

4 citations