Previously, we published an analysis of 149 genomes of 78 different species isolated from the female bladder [14]. Several of the taxa found within the bladder microbiota are also inhabitants of the vaginal microbiota [14,21,22]. This led us to posit that the bacterial communities of these t...
Although restriction enzymes are widely used in molecular cloning, their use as molecular tools extends to other common applications in molecular biology. Two important applications are DNA fingerprinting and methylation analysis, ...
hytes are more closely related to conifers (the “Gnepine”, “Gnecup” or “Gnetifer” hypotheses) than to other gymnosperms7. In this work, we use genome assembly data together with extensive epigenomic and transcriptomic data to unveil a distinctive genome structure that enhances our unders...
TheS.agalactiaepan-genome is ‘open’; theB.anthracisone is ‘closed’. After sequencing a large number of strains, the number of dispensable genes in an open pan-genome is orders of magnitude larger than the size of the core genome, forcing us to reconsider the definition of a bacterial ...
heatmap showing the ancestral gene and gained events for each genus. The top lines represent the functional category of orthologous genes in each column and are colored according to the COG annotations. The number of gene gain events among different genera is shown on the line plot. CPS, ...
The circular map ofCalophyllum soulattrimitochondrial genome. The gray arrows show the direction of transcription. Genes inside the circle are transcribed clockwise while genes outside the circle are transcribed counterclockwise. The gray bars inside the circle represent the GC content of the sequence....
CRISPRmap - [webserver] - CRISPRmap provides a quick and detailed insight into repeat conservation and diversity of both bacterial and archaeal systems. CRISPRone - [webserver(database)] - A database provides annotation of CRISPR—Cas systems including: CRISPR arrays of repeat-spacer units and ...
The “Recurrent genes” heatmap presents the 24 most recurrently mutated genes, each with at least three samples in each hyper-SV group. Coding, SNVs/indels in coding region; Noncoding, SNVs/indels in noncoding region; HRPCa, high-risk PCa; IRPCa, intermediate-risk PCa; LRPCa, low-...
[43] global was used to map the paired-end Hi-C reads to the draft assembled genome. The resulting paired-end Hi-C reads were used to cluster, orient, and link the assembled contigs into pseudochromosomes using YaHS (version 1.1) [44] and Endhic [45]. Finally, the integrity of the...
The strains corresponding to the different metabolic regimes (blue and red dots in a) map onto different regions in the space of objectives, labeled with similar colors Full size image Upon applying invFBA to the complete set of measured flux data (Additional file 8: Table S4 and Additional ...