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The methods describe in this paper will be useful for sequencing genomes of individual cells from a variety of samples.
This strategy is useful for sequencing data with a reasonable level of coverage from a single individual, because false positives of base positions will be quite low and differentiation between individuals does not need to be considered.
The method proved useful for sequencing C. trachomatis from complex clinical samples but required in excess of 1,500,000 genome copies per microliter, following whole genome amplification, and sequencing on an Illumina HiSeq to generate sufficient numbers of reads for C. trachomatis genome mapping.
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In addition to the estimation of base-calling parameters, a control lane also provides useful statistics for sequencing quality.
It may also be used in species without a reference genome sequence, although a reference genome is useful for sequence alignment, SNP ordering (if imputation or GWAS are to be used) and for quality control.
"By-sequence" definitions that attribute terminal extensions to the sequence-continuous polypeptide segment (similar to SCOP) are more useful for sequence search strategies; as such regions may contain conserved sequence motifs.
Among the three major categories of phylogenetic inference methods, distance, maximum parsimony (MP), and maximum likelihood (ML), ML methods are especially useful for sequence sets with varying extents of sequence diversity [2], [3].
At the time when these sequence searches were done, this database had been shown to contain higher diversity, useful for sequence bioprospecting [ 32, 43].
It should also be highlighted that the chromosome-sized scaffolds of T. cruzi are useful for sequence analysis and constitute an important tool for defining the linear gene sequence of the parasite.
For a number of problems, the existence of curated databases including only contextual data, useful for sequence and functional annotation, can play an important roll for denoising data analysis results and highlight small but important signals in the data.
Since much of these remaining data can be unambiguously mapped despite having ≥4 mismatches (Table 1), and are therefore useful for sequence census methods, we sought to develop a tool that would allow mapping of SOLiD sequence data in a more flexible, mismatch-tolerant context that would maximize the number of usable sequences within a given dataset.
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