PHI-base: a new interface and further additions for the multi-species pathogen-host interactions database
The pathogen–host interactions database (PHI-base) is available at www.phi-base.org. PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen–host interactions reported in peer reviewed research articles. In addition, literature that indicates specific gene alterations that did not affect the disease interaction phenotype are curated to provide complete datasets for comparative purposes. Viruses are not included. Here we describe a revised PHI-base Version 4 data platform with improved search, filtering and extended data display functions. A PHIB-...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Urban, M., Cuzick, A., Rutherford, K., Irvine, A., Pedro, H., Pant, R., Sadanadan, V., Khamari, L., Billal, S., Mohanty, S., Hammond-Kosack, K. E. Tags: Database Issue Source Type: research
The PathoYeastract database: an information system for the analysis of gene and genomic transcription regulation in pathogenic yeasts
We present the PATHOgenic YEAst Search for Transcriptional Regulators And Consensus Tracking (PathoYeastract - http://pathoyeastract.org) database, a tool for the analysis and prediction of transcription regulatory associations at the gene and genomic levels in the pathogenic yeasts Candida albicans and C. glabrata. Upon data retrieval from hundreds of publications, followed by curation, the database currently includes 28 000 unique documented regulatory associations between transcription factors (TF) and target genes and 107 DNA binding sites, considering 134 TFs in both species. Following the structure used for the YEAST...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Monteiro, P. T., Pais, P., Costa, C., Manna, S., Sa-Correia, I., Teixeira, M. C. Tags: Database Issue Source Type: research
The Candida Genome Database (CGD): incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data
The Candida Genome Database (CGD, http://www.candidagenome.org/) is a freely available online resource that provides gene, protein and sequence information for multiple Candida species, along with web-based tools for accessing, analyzing and exploring these data. The mission of CGD is to facilitate and accelerate research into Candida pathogenesis and biology, by curating the scientific literature in real time, and connecting literature-derived annotations to the latest version of the genomic sequence and its annotations. Here, we report the incorporation into CGD of Assembly 22, the first chromosome-level, phased diploid ...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Skrzypek, M. S., Binkley, J., Binkley, G., Miyasato, S. R., Simison, M., Sherlock, G. Tags: Database Issue Source Type: research
MEGARes: an antimicrobial resistance database for high throughput sequencing
Antimicrobial resistance has become an imminent concern for public health. As methods for detection and characterization of antimicrobial resistance move from targeted culture and polymerase chain reaction to high throughput metagenomics, appropriate resources for the analysis of large-scale data are required. Currently, antimicrobial resistance databases are tailored to smaller-scale, functional profiling of genes using highly descriptive annotations. Such characteristics do not facilitate the analysis of large-scale, ecological sequence datasets such as those produced with the use of metagenomics for surveillance. In ord...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Lakin, S. M., Dean, C., Noyes, N. R., Dettenwanger, A., Ross, A. S., Doster, E., Rovira, P., Abdo, Z., Jones, K. L., Ruiz, J., Belk, K. E., Morley, P. S., Boucher, C. Tags: Database Issue Source Type: research
IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes
Secondary metabolites produced by microbes have diverse biological functions, which makes them a great potential source of biotechnologically relevant compounds with antimicrobial, anti-cancer and other activities. The proteins needed to synthesize these natural products are often encoded by clusters of co-located genes called biosynthetic gene clusters (BCs). In order to advance the exploration of microbial secondary metabolism, we developed the largest publically available database of experimentally verified and predicted BCs, the Integrated Microbial Genomes Atlas of Biosynthetic gene Clusters (IMG-ABC) (https://img.jgi...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Hadjithomas, M., Chen, I.-M. A., Chu, K., Huang, J., Ratner, A., Palaniappan, K., Andersen, E., Markowitz, V., Kyrpides, N. C., Ivanova, N. N. Tags: Database Issue Source Type: research
The antiSMASH database, a comprehensive database of microbial secondary metabolite biosynthetic gene clusters
Secondary metabolites produced by microorganisms are the main source of bioactive compounds that are in use as antimicrobial and anticancer drugs, fungicides, herbicides and pesticides. In the last decade, the increasing availability of microbial genomes has established genome mining as a very important method for the identification of their biosynthetic gene clusters (BGCs). One of the most popular tools for this task is antiSMASH. However, so far, antiSMASH is limited to de novo computing results for user-submitted genomes and only partially connects these with BGCs from other organisms. Therefore, we developed the antiS...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Blin, K., Medema, M. H., Kottmann, R., Lee, S. Y., Weber, T. Tags: Database Issue Source Type: research
CyanoBase: a large-scale update on its 20th anniversary
The first ever cyanobacterial genome sequence was determined two decades ago and CyanoBase (http://genome.microbedb.jp/cyanobase), the first database for cyanobacteria was simultaneously developed to allow this genomic information to be used more efficiently. Since then, CyanoBase has constantly been extended and has received several updates. Here, we describe a new large-scale update of the database, which coincides with its 20th anniversary. We have expanded the number of cyanobacterial genomic sequences from 39 to 376 species, which consists of 86 complete and 290 draft genomes. We have also optimized the user interface...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Fujisawa, T., Narikawa, R., Maeda, S.-i., Watanabe, S., Kanesaki, Y., Kobayashi, K., Nomata, J., Hanaoka, M., Watanabe, M., Ehira, S., Suzuki, E., Awai, K., Nakamura, Y. Tags: Database Issue Source Type: research
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes
The availability of microbial genomes has opened many new avenues of research within microbiology. This has been driven primarily by comparative genomics approaches, which rely on accurate and consistent characterization of genomic sequences. It is nevertheless difficult to obtain consistent taxonomic and integrated functional annotations for defined prokaryotic clades. Thus, we developed proGenomes, a resource that provides user-friendly access to currently 25 038 high-quality genomes whose sequences and consistent annotations can be retrieved individually or by taxonomic clade. These genomes are assigned to 5306 consiste...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Mende, D. R., Letunic, I., Huerta-Cepas, J., Li, S. S., Forslund, K., Sunagawa, S., Bork, P. Tags: Database Issue Source Type: research
MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes
The annotation of genomes from NGS platforms needs to be automated and fully integrated. However, maintaining consistency and accuracy in genome annotation is a challenging problem because millions of protein database entries are not assigned reliable functions. This shortcoming limits the knowledge that can be extracted from genomes and metabolic models. Launched in 2005, the MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. Effective comparative analysis requi...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Vallenet, D., Calteau, A., Cruveiller, S., Gachet, M., Lajus, A., Josso, A., Mercier, J., Renaux, A., Rollin, J., Rouy, Z., Roche, D., Scarpelli, C., Medigue, C. Tags: Database Issue Source Type: research
IMG/M: integrated genome and metagenome comparative data analysis system
The Integrated Microbial Genomes with Microbiome Samples (IMG/M: https://img.jgi.doe.gov/m/) system contains annotated DNA and RNA sequence data of (i) archaeal, bacterial, eukaryotic and viral genomes from cultured organisms, (ii) single cell genomes (SCG) and genomes from metagenomes (GFM) from uncultured archaea, bacteria and viruses and (iii) metagenomes from environmental, host associated and engineered microbiome samples. Sequence data are generated by DOE's Joint Genome Institute (JGI), submitted by individual scientists, or collected from public sequence data archives. Structural and functional annotation is carrie...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Chen, I.-M. A., Markowitz, V. M., Chu, K., Palaniappan, K., Szeto, E., Pillay, M., Ratner, A., Huang, J., Andersen, E., Huntemann, M., Varghese, N., Hadjithomas, M., Tennessen, K., Nielsen, T., Ivanova, N. N., Kyrpides, N. C. Tags: Database Issue Source Type: research
The Papillomavirus Episteme: a major update to the papillomavirus sequence database
The Papillomavirus Episteme (PaVE) is a database of curated papillomavirus genomic sequences, accompanied by web-based sequence analysis tools. This update describes the addition of major new features. The papillomavirus genomes within PaVE have been further annotated, and now includes the major spliced mRNA transcripts. Viral genes and transcripts can be visualized on both linear and circular genome browsers. Evolutionary relationships among PaVE reference protein sequences can be analysed using multiple sequence alignments and phylogenetic trees. To assist in viral discovery, PaVE offers a typing tool; a simplified algor...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Van Doorslaer, K., Li, Z., Xirasagar, S., Maes, P., Kaminsky, D., Liou, D., Sun, Q., Kaur, R., Huyen, Y., McBride, A. A. Tags: Database Issue Source Type: research
Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation
Viruses are the most abundant and diverse biological entities on earth, and while most of this diversity remains completely unexplored, advances in genome sequencing have provided unprecedented glimpses into the virosphere. The Prokaryotic Virus Orthologous Groups (pVOGs, formerly called Phage Orthologous Groups, POGs) resource has aided in this task over the past decade by using automated methods to keep pace with the rapid increase in genomic data. The uses of pVOGs include functional annotation of viral proteins, identification of genes and viruses in uncharacterized DNA samples, phylogenetic analysis, large-scale compa...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Grazziotin, A. L., Koonin, E. V., Kristensen, D. M. Tags: Database Issue Source Type: research
Virus Variation Resource - improved response to emergent viral outbreaks
The Virus Variation Resource is a value-added viral sequence data resource hosted by the National Center for Biotechnology Information. The resource is located at http://www.ncbi.nlm.nih.gov/genome/viruses/variation/ and includes modules for seven viral groups: influenza virus, Dengue virus, West Nile virus, Ebolavirus, MERS coronavirus, Rotavirus A and Zika virus. Each module is supported by pipelines that scan newly released GenBank records, annotate genes and proteins and parse sample descriptors and then map them to controlled vocabulary. These processes in turn support a purpose-built search interface where users can ...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Hatcher, E. L., Zhdanov, S. A., Bao, Y., Blinkova, O., Nawrocki, E. P., Ostapchuck, Y., Schäffer, A. A., Brister, J. R. Tags: Database Issue Source Type: research
MRPrimerV: a database of PCR primers for RNA virus detection
Many infectious diseases are caused by viral infections, and in particular by RNA viruses such as MERS, Ebola and Zika. To understand viral disease, detection and identification of these viruses are essential. Although PCR is widely used for rapid virus identification due to its low cost and high sensitivity and specificity, very few online database resources have compiled PCR primers for RNA viruses. To effectively detect viruses, the MRPrimerV database (http://MRPrimerV.com) contains 152 380 247 PCR primer pairs for detection of 1818 viruses, covering 7144 coding sequences (CDSs), representing 100% of the RNA viruses in ...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Kim, H., Kang, N., An, K., Kim, D., Koo, J., Kim, M.-S. Tags: Database Issue Source Type: research
Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements
The Genomes Online Database (GOLD) (https://gold.jgi.doe.gov) is a manually curated data management system that catalogs sequencing projects with associated metadata from around the world. In the current version of GOLD (v.6), all projects are organized based on a four level classification system in the form of a Study, Organism (for isolates) or Biosample (for environmental samples), Sequencing Project and Analysis Project. Currently, GOLD provides information for 26 117 Studies, 239 100 Organisms, 15 887 Biosamples, 97 212 Sequencing Projects and 78 579 Analysis Projects. These are integrated with over 312 metadata field...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Mukherjee, S., Stamatis, D., Bertsch, J., Ovchinnikova, G., Verezemska, O., Isbandi, M., Thomas, A. D., Ali, R., Sharma, K., Kyrpides, N. C., Reddy, T. B. K. Tags: Database Issue Source Type: research
