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19
doi:10.1093/nar/gkr990 The UCSC Archaeal Genome Browser: 2012 update
, 2011
"... The UCSC Archaeal Genome Browser ..."
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doi:10.1093/nar/gkq1268 RATT: Rapid Annotation Transfer Tool
, 2010
"... Second-generation sequencing technologies have made large-scale sequencing projects commonplace. However, making use of these datasets often requires gene function to be ascribed genome wide. Although tool development has kept pace with the changes in sequence production, for tasks such as mapping, ..."
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Cited by 12 (5 self)
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Second-generation sequencing technologies have made large-scale sequencing projects commonplace. However, making use of these datasets often requires gene function to be ascribed genome wide. Although tool development has kept pace with the changes in sequence production, for tasks such as mapping, de novo assembly or visualization, genome annotation remains a challenge. We have developed a method to rapidly provide accurate annotation for new genomes using previously annotated genomes as a reference. The method, implemented in a tool called RATT (Rapid Annotation Transfer Tool), transfers annotations from a high-quality reference to a new genome on the basis of conserved synteny. We demonstrate that a Mycobacterium tuberculosis genome or a single 2.5 Mb chromosome from a malaria parasite can be annotated in less than five minutes with only modest computational resources. RATT is available at
FungiDB: an integrated functional genomics database for fungi
, 2011
"... FungiDB ..."
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Comparative metagenomics of two microbial mats at Cuatro Ciénegas Basin I: ancient lessons on how to cope with an environment under severe nutrient stress. Astrobiology 12:648–658
, 2012
"... Microbial mats are self-sustained, functionally complex ecosystems that make goodmodels for the understanding of past and presentmicrobial ecosystems aswell as putative extraterrestrial ecosystems. Ecological theory suggests that the composition of these communitiesmight be affected bynutrient avail ..."
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Microbial mats are self-sustained, functionally complex ecosystems that make goodmodels for the understanding of past and presentmicrobial ecosystems aswell as putative extraterrestrial ecosystems. Ecological theory suggests that the composition of these communitiesmight be affected bynutrient availability anddisturbance frequency.We characterized twomicrobial mats from two contrasting environments in the oligotrophic Cuatro Ciénegas Basin: a permanent green pool and a red desiccation pond. We analyzed their taxonomic structure and composition by means of 16S rRNA clone libraries andmetagenomics and inferred theirmetabolic role by the analysis of functional traits in themost abundant organisms. Bothmats showed a high diversitywithmetabolically diversemembers and strongly differed in structure and composition. The green mat had a higher species richness and evenness than the red mat, which was dominated by a lineage of Pseudomonas. Autotrophs were abundant in the green mat, and heterotrophs were abundant in the red mat. When comparing with other mats and stromatolites, we found that taxonomic compositionwas not shared at species level but at order level,which suggests environmental filtering for phylogenetically conserved functional traits with random selection of particular organisms. The highest diversity and composition similarity was observed among systems from stable environments, which suggests that distur-bance regimes might affect diversity more strongly than nutrient availability, since oligotrophy does not appear to prevent the establishment of complex and diverse microbial mat communities. These results are discussed in light of the search for extraterrestrial life. Key Words: Cuatro Ciénegas—Metagenomics—Microbial mats— Oligotrophic—Phosphorus limitation—Stromatolites. Astrobiology 12, 659–673. 1.
Genome analysis Advance Access publication July 15, 2011
"... PGAT: a multistrain analysis resource for microbial genomes ..."
iii Table of Contents
, 2013
"... To my wife Ge, my parents Songjuan and Xianhui, and to my professors and friends. ..."
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To my wife Ge, my parents Songjuan and Xianhui, and to my professors and friends.
2011 DoD High Performance Computing Modernization Program Users Group Conference A Web-based High-Throughput Tool for Next-Generation Sequence Annotation
"... The availability of a large number of genome sequences, resulting from inexpensive, high-throughput next-generation sequencing platforms, has created the need for an integrated, fully-automated, rapid, and high-throughput annotation capability that is also easy-to-use. Here, we present a web-based s ..."
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The availability of a large number of genome sequences, resulting from inexpensive, high-throughput next-generation sequencing platforms, has created the need for an integrated, fully-automated, rapid, and high-throughput annotation capability that is also easy-to-use. Here, we present a web-based software application, Annotation of Genome Sequences (AGeS), which incorporates publicly-available and in-house-developed bioinformatics tools and databases, many of which are parallelized for high-throughput performance. The current version of AGeS provides annotations for bacterial genome sequences, and serves as a readily-accessible resource to Department of Defense (DoD) scientists for storing, annotating, and visualizing genomes of newly-sequenced pathogens of interest. The AGeS system is composed of two major components. The first component is a web-based application that provides a graphical user interface for managing users ’ input genomes, submitting annotation jobs, and visualizing results. Sequence contigs are uploaded as a multi-FASTA input file and submitted for annotation, and the resulting annotations are visualized through GBrowse. The input genome sequences and the annotation results are stored in a secure, customized database. The second component is a high-throughput annotation pipeline for finding the genomic regions that code for proteins, RNAs, and other genomic elements through a Do-It-Yourself Annotation framework. The pipeline also functionally annotates the protein-coding regions using an in-house-developed high-throughput pipeline, the Pipeline for Protein Annotation. The
Southampton, UK Reviewed by:
, 2012
"... doi: 10.3389/fmicb.2012.00142 Mining genomes of marine cyanobacteria for elements of zinc homeostasis ..."
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doi: 10.3389/fmicb.2012.00142 Mining genomes of marine cyanobacteria for elements of zinc homeostasis
