Analysis Results for BRC-Microbial Genomes
Novel lantibiotics from microbial genomes
... bioinformatic analysis the partial mersacidin gene cluster, identified in ...detailed analysis of both mrsG DNA sequences indicated, that a thymidine residue was missing in position 980 of the original ...
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Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0.
... of microbial diversity affecting the human body and the ...in microbial genomics, for contextualizing genomes without prior phenotypic information, and for determining their genetic novelty and ...
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Short segmental duplication: parsimony in growth of microbial genomes
... textual analysis of DNA sequences and, with the success of the Human Genome Project, such activities have intensified with ...of analysis that, as far as the authors are aware, has not been reported in the ...
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Self-identification of protein-coding regions in microbial genomes
... Preliminary Results with Less Compact ...the analysis of new bacterial genomes. Its extension to the analysis of less compact genomes is being ...complex genomes thus might be ...
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From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer
... all genomes as a vector yp and solved a binary classification problem by using the matrix of Pfam phyletic patterns XP across all genomes as input features and yp as the binary target variable (see ...
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Mining microbial genomes for new natural products and biosynthetic pathways
... Sequence analysis of the intergenic regions between the cchA and cchB genes, and the cchH and cchI genes, showed that they contained inverted repeat sequences similar to known binding sites for ferrous ...
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Reducing assembly complexity of microbial genomes with single molecule sequencing
... The CCS correction also underperformed the other methods, likely due to its lower per-read accuracy. Most promising, the self-corrected CLR sequences produced the fewest errors, even outperforming assemblies that in- ...
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Uncovering metabolic pathways relevant to phenotypic traits of microbial genomes
... tistical analysis of metabolic pathways for 266 sequenced genomes, our method automatically finds pathways that are supposed to be relevant for a special phenotypic ...association analysis to a ...
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The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes
... crobial Genomes, IMG-ER: IMG Expert Review, CRISPR: Clustered Regularly Interspaced Short Palindromic Repeats, MAP Microbial Annotation ...DOE-JGI Microbial Annotation Pipeline (DOE-JGI MAP) supports ...
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Genomes of the T4 related bacteriophages as windows on microbial genome evolution
... two genomes does not explain why RB69 completely excludes T4 ...T4-related genomes from par- tial to total genetic isolation from each other despite access to the same bacterial host ...genome ...
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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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Spectrogram Analysis of Genomes
... CpG islands [13] are DNA stretches in which a partic- ular methylation process that normally reduces the occur- rence of CG dinucleotides is suppressed, and therefore CG nucleotides appear more frequently than elsewhere. ...
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From single genomes to natural microbial communities : novel methods for the high-throughput analysis of genomic sequences
... of microbial genes in the space of sequence composition is affected by various influ- ences that are pronounced to different extent for different genomes and thus require a careful and time-consuming anal- ...
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IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes.
... Selected Genomes, 16S RNA, Virus (28), CRISPR Spacers, and All ...Selected Genomes option, IMG enables protein, nucleotide and translated BLAST search of a user- submitted sequence against a ...
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Migration and horizontal gene transfer divide microbial genomes into multiple niches
... in microbial ecology 45,46 and allowing migration in our model results in large amounts of horizontal transfer that has the power to transform the genomics of the ...
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An environmental signature for 323 microbial genomes based on codon adaptation indices
... bacterial genomes, as well as five fungal genomes, we show that codon usage preference provides an environmental signature by which it is possible to group bacteria according to their lifestyle, for ...
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Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen
... . Genomes and gene predictions were loaded into a Meta4 database 77 The cleaned bins were compared, using MinHash sketches as implemented in Sourmash 78 , to 100,000 genomes in GenBank; 410 genomes ...
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Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics
... reconstructing microbial genomes from soil using metagenomics have been challenging due to the tremendous diversity and relatively uniform distribution of genomes found in this ...metagenomic ...
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The Integrated Microbial Genomes (IMG) System: A Case Study in Biological Data Management
... and analysis operations and were developed without considering data analysis workflows, heterogeneity, evolution, and scalability ...domain analysis process and comprehensive documentation are ...
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A de Bruijn graph approach to the quantification of closely-related genomes in a microbial community
... coli genomes using different coverages ranging from 0 to 40 · ...the results of BWA with the conventional alignment tool BLAST, in terms of the number of mapped reads and the quantification ...
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