Microbial genomes
Migration and horizontal gene transfer divide microbial genomes into multiple niches
... to microbial evolution, because it enables genetic regions to spread horizontally through diverse ...way, microbial genomes can evolve to become ecologically diverse where different genomic regions ...
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The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes
... DOE-JGI Microbial Annotation Pipeline (DOE-JGI MAP) supports gene prediction and/or functional annotation of microbial genomes towards comparative analysis with the Integrated Microbial Genome ...
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The Harvest suite for rapid core genome alignment and visualization of thousands of intraspecific microbial genomes
... align genomes of any size; how- ever, the current implementation has been optimized for microbial genomes, requiring approximately 32 bytes per reference base for CSG construction and 15 bytes per ...
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k-mer Similarity, Networks of Microbial Genomes, and Taxonomic Rank
... ABSTRACT Microbial genomes have been shaped by parent-to-offspring (verti- cal) descent and lateral genetic ...archaeal genomes and compared the contributions of rRNA, protein-coding, and plasmid ...
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Mining microbial genomes for new natural products and biosynthetic pathways
... Many microbial natural products, in particular complex polyketides and nonribosomal peptides, are assembled by biosynthetic assembly lines involving modular mega- synthases and synthetases (Fischbach & Walsh, ...
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High quality draft genome sequence of Bacteroides barnesiae type strain BL2T (DSM 18169T) from chicken caecum
... thousand microbial genomes project [9] which aims not only to increase the sequencing coverage of key reference microbial ge- nomes [15], but also to generate a large genomic basis for the discovery ...
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Draft genome sequence of Rubidibacter lacunae strain KORDI 51-2T, a cyanobacterium isolated from seawater of Chuuk lagoon
... The gene prediction and functional annotation of the genome sequence was basically performed within the Integrated Microbial Genomes – Expert Review (IMG-ER) platform [11]. The tRNAScan-SE was used to find ...
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High quality draft genome sequence of Brachymonas chironomi AIMA4T (DSM 19884T) isolated from a Chironomus sp. egg mass
... Brachymonas chironomi strain AIMA4 T (Halpern et al., 2009) is a Gram-negative, non-motile, aerobic, chemoorganotroph bacterium. B. chironomi is a member of the Comamonadaceae, a family within the class ...
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Complete genome sequence of Sanguibacter keddieii type strain (ST-74T)
... (http://geneprimp.jgi-psf.org) [ 24 ]. The predicted coding sequences (CDS)s were translated and used to search the National Center for Biotechnol- ogy Information (NCBI) nonredundant database, UniProt, TIGRFam, Pfam, ...
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Identification of microbial DNA in human cancer
... DNA microbial genomes that are not actively ...rare microbial associations through extraction of sequences from specific locations in microbial ...
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Complete Genome sequence of Burkholderia phymatum STM815T, a broad host range and efficient nitrogen-fixing symbiont of Mimosa species
... Automatic annotation was performed using the In- tegrated Microbial Genomes (IMG) platform [36] developed by the Joint Genome Institute, Walnut Creek, CA, USA [28].. Addi[r] ...
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Complete genome sequence of Halogeometricum borinquense type strain (PR3T)
... Genes were identified using GeneMark [ 21 ] as part of the genome annotation pipeline in the Inte- grated Microbial Genomes Expert Review (IMG-ER) system [ 22 ], followed by a round of[r] ...
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Complete genome sequence of Saccharomonospora viridis type strain (P101T)
... Genes were identified using GeneMark [ 26 ] as part of the genome annotation pipeline in the Inte- grated Microbial Genomes Expert Review (IMG-ER) system [ 27 ], followed by a round of manual cura- tion ...
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Draft genome sequences and description of Lactobacillus rhamnosus strains L31, L34, and L35
... Open Reading Frames (ORFs) were predicted us- ing Prodigal [33,34] as part of the Oak Ridge Na- tional Laboratory genome annotation pipeline, fol- lowed by a round of manual curation using the JGI GenePRIMP pipeline ...
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High-quality permanent draft genome sequence of the extremely osmotolerant diphenol degrading bacterium Halotalea alkalilenta AW-7T, and emended description of the genus Halotalea
... thousand microbial genomes (KMG) project at the DOE Joint Genome Institute, and it is the only strain within the genus Halotalea having its genome ...
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Quality scores for 32,000 genomes
... of genomes submitted to public re- ...finishing genomes. Finishing second- generation sequenced genomes continues to be expen- sive and many researchers have no plans to finish their draft ...
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Complete genome sequence of Arthrobacter sp. strain FB24
... the genomes of these strains were made and visualized using hi- erarchical clustering (Figure 5) with tools availa- ble on the Joint Genome Institute (JGI) Integrated Microbial Genomes (IMG) ...
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Genomes of the T4 related bacteriophages as windows on microbial genome evolution
... DNA genomes and the predicted compositions of their proteomes. The genomes of about 40 of these phages have been sequenced and annotated over the last several years and are compared here in the con- text of ...
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High quality draft genome sequence of Leucobacter chironomi strain MM2LBT (DSM 19883T) isolated from a Chironomus sp. egg mass
... Leucobacter chironomi strain MM2LB T (Halpern et al., Int J Syst Evol Microbiol 59:665-70 2009) is a Gram-positive, rod shaped, non-motile, aerobic, chemoorganotroph bacterium. L. chironomi belongs to the family ...
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Metagenomics for Clinical Infectious Disease Diagnostics Steps Closer to Reality
... of microbial genomes (without amplification of background human DNA), they generally allow taxonomic identification at a significantly lower depth of sequencing than shotgun-based approaches, with typical ...
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