Coverage for each G. stearothermophilus genome sequenced
Genome Rearrangements of Completely Sequenced Strains of Yersinia pestis
... ships among Y. pestis species. Each genome plate can change its location and orientation in the genomes of Y. pestis. How- ever, the gene content between the plate and its counterpart is almost consistent. ...
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Multilocus Sequence Typing of Total Genome Sequenced Bacteria
... For a specific MLST scheme, the MLST alleles of each locus are aligned to the genome by using BLAST. The closest-matching MLST allele is selected, and the ST is determined based on the combination of MLST ...
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A daily-updated tree of (sequenced) life as a reference for genome research
... low coverage and poorly assembled genomes, as can be seen in many cases by the lack of essen- tial ribosomal and house-keeping ...of genome assemblies are again likely to be the cause of the ...the ...
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Variation in mitochondrial genome primary sequence among whole-genome-sequenced strains of Neurospora crassa
... has seen a resurgence of interest as degraded mitochondria CQ9 7 2 &!!# 49 O et al. &!! Filamentous fungi have been described as providing a good model for the study of mitochondrial inheritance and 3##60 genome ...
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Whole-genome assembly of Akkermansia muciniphila sequenced directly from human stool
... Authors’ response: There is a logical order of applica- tions for the mapping approach. This approach involves aligning reads against a reference genome. We started with the longer reads from the 454 shotgun data ...
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Patchwork: allele specific copy number analysis of whole genome sequenced tumor tissue
... malized coverage, corresponding to one copy in the tumor cells, and Δ exp , which is the difference that can be expected in a sample with 100% pure tumor ...normalized coverage, and loss or gain of one copy ...
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Genome wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli
... patterns. Each of these score functions assigns an integer value to each SND ...by each function to consecutive SNDs in the ...for each of the three topologies are plotted concurrently in ...
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Comparative Functional Study of Thioester-containing Related Proteins in the Recently Sequenced Genome of Biomphalaria glabrata
... of each protein was predicted us- ing an advanced protein subcellular localiza- tion prediction tool; WoLF ...of each protein were obtained from Pfam ...
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In silico analysis highlights the frequency and diversity of type 1 lantibiotic gene clusters in genome sequenced bacteria
... the genome viewer on NCBI, and indivi- dual orfs were subjected to BLAST analysis to identify those potentially involved in lantibiotic production or ...were each in turn used for further in silico screens ...
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A strategy to improve phasing of whole-genome sequenced individuals through integration of familial information from dense genotype panels.
... To evaluate the impact of the pre-phasing strategy on imputation accuracy, a 13-fold cross-validation was per- formed. The imputation to seven target animals from 84 reference animals was repeated 13 times. Pools of ...
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A high-coverage genome sequence from an archaic denisovan individual
... We sequenced these libraries from both ends using Illumina’s Ge- nome Analyzer IIx and included reads for two indexes (11), which were added in the clean room to exclude the possibility of down- stream ...
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Glucose metabolism ontogenesis in rainbow trout (Oncorhynchus mykiss) in the light of the recently sequenced genome: new tools for intermediary metabolism programming
... described above. Care was taken to maintain the same daily time frame before samplings to avoid potential circadian effects, known to affect metabolism in rainbow trout (Bolliet et al., 2000). Fish were therefore ...
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A Novel Approach to Estimating Heterozygosity from Low-Coverage Genome Sequence
... been sequenced at ,10X coverage and provides reasonable esti- mates for as low as 4X ...other sequenced individ- uals from the same population or when the population is ...
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Information recovery from low coverage whole-genome bisulfite sequencing
... of coverage after downsampling IHEC replicate methylomes M7–10 against deep replicates M1–2 as part of a separate saturation analysis 8 ...For each methylome, the number of iCGs, DMPs, DMRs, COMETs and DMCs ...
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Understand Effective Coverage by Mapped Reads using Genome Repeat Complexity
... between genome effective coverage and repeat ...effective coverage by mapped reads for each short-read ...effective coverage of genomes given a sequencing depth might help researchers ...
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Completely sequenced genomes of pathogenic bacteria: A review
... a genome include more accurate disease diag- nosis by identifying unique sequence candidates for PCR-based assays, and finding candidates for immunodi- agnostic tests by heterologous expression of each ...
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Precise A•T to G•C base editing in the zebrafish genome
... The targeted genomic loci were amplified from genomic DNA and the PCR products were used for both direct se- quencing and T-A cloning/sequencing. For PCR direct products sequencing, we evaluated three groups (6 em- bryos ...
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Low coverage whole genome sequencing enables accurate assessment of common variants and calculation of genome-wide polygenic scores
... at each of the biallelic SNP loci in the imputation SNP loci that were covered by one or more sequencing reads called using the mpileup command implemented in bcftools version ...at each observed site were ...
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The Human Genome Was Never Completely Sequenced - Scientific American
... weren’t sequenced by either the genome project or a later effort called the 1000 Genomes Project, “have been missed,” Eichler and his colleagues reported last ...
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In and out of the rRNA genes: characterization of Pokey elements in the sequenced Daphnia genome
... pulex genome and the raw trace files revealed that rDNA units display extremely low levels of sequence variation consistent with the high rates of recombination previously observed for this ...
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