Showing papers on "Munich Information Center for Protein Sequences published in 2014"

MycoCosm portal: gearing up for 1000 fungal genomes

Abstract: MycoCosm is a fungal genomics portal (http://jgi.doe.gov/fungi), developed by the US Department of Energy Joint Genome Institute to support integration, analysis and dissemination of fungal genome sequences and other 'omics' data by providing interactive web-based tools. MycoCosm also promotes and facilitates user community participation through the nomination of new species of fungi for sequencing, and the annotation and analysis of resulting data. By efficiently filling gaps in the Fungal Tree of Life, MycoCosm will help address important problems associated with energy and the environment, taking advantage of growing fungal genomics resources.

In search of genome annotation consistency: solid gene clusters and how to use them.

Abstract: Maintaining consistency in genome annotations is important for supporting many computational tasks, particularly metabolic modeling. The SEED project has implemented a process that improves annotation consistencies across microbial genomes for proteins with conserved sequences and genomic context. In this research report, we describe this process and show how this effort has resulted in improvements to microbial genome annotations in the SEED. We also compare SEED annotation consistencies with other commonly used resources such as IMG (the Joint Genome Institute’s Integrated Microbial Genomes system), RefSeq (the National Center for Biotechnology Information’s Reference Sequence Database), Swiss-Prot (the annotated protein sequence database of the Swiss Institute of Bioinformatics, European Molecular Biology Laboratory and the European Bioinformatics Institute) and TrEMBL (Translated European Molecular Biology Laboratory nucleotide sequence data Library). Our analysis indicates that manual and computational efforts are paying off for the databases where consistency is a major goal.

DENVirDB: a web portal of dengue virus sequence information on Asian isolates.

Abstract: DENVirDB is a web portal that provides the sequence information and computationally curated information of dengue viral proteins. The advent of genomic technology has increased the sequences available in the public databases. In order to create relevant concise information on Dengue Virus (DENV), the genomic sequences were collected, analysed with the bioinformatics tools and presented as DENVirDB. It provides the comprehensive information of complete genome sequences of dengue virus isolates of Southeast Asia, viz. India, Bangladesh, Sri Lanka, East Timor, Philippines, Malaysia, Papua New Guinea, Brunei and China. DENVirDB also includes the structural and non-structural protein sequences of DENV. It intends to provide the integrated information on the physicochemical properties, topology, secondary structure, domain and structural properties for each protein sequences. It contains over 99 entries in complete genome sequences and 990 entries in protein sequences, respectively. Therefore, DENVirDB could serve as a user friendly database for researchers in acquiring sequences and proteomic information in one platform.