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An assessment of the sequence gaps: unfinished business in a finished human genome.
Lambert, N. et al. RNA Bind-n-Seq: quantitative assessment of the sequence and structural binding specificity of RNA binding proteins.
The assessment of the sequence quality was performed via the CCBC automated informatics pipeline following the guidelines of the CBOL (2009).
Initial processing and quality assessment of the sequence data was performed using a software pipeline developed at the Centre for Genomic Research, University of Liverpool (Dr. Richard Gregory, personal communication).
Although entropy is commonly used to evaluate sequence conservation in an alignment [ 36- 38] and to compare simulated data with natural sequences [ 39, 40], it is not enough for a thorough assessment of the sequence pattern.
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Furthermore, analysis of read abundances of sequence variants allowed an assessment of the sequencing error rates independent of those supplied in sequence quality files.
Quality assessment of the sequencing data (in FASTQ format) was done using FASTQC [ 31], followed by trimming of adapters and low-quality bases with a Phred quality score of less than 20 and filtering for a minimum read length of 36 using Trimmomatic [ 32].
Since only 20 (400) double mutants are possible per pairwise sequence randomized, this strategy allowed us to perform an initial assessment of the absolute sequence selectivity at five different positions with a potential library size of 1200 sequences, rather than 3.2 million.
Assessment of the Cys1 sequence properties failed to result into a reliable 3D model.
Consistent failure of crystallization efforts with eukaryotic Pur-α prompted us to perform bioinformatics assessment of the protein sequence.
After detailed assessment of the tRNA sequence, the high frequency of "U" at the 5'-end of 22nt RNA arise from a nucleotide corresponding to the position 54 of tRNA, which is commonly "U" in all of the tRNAs.
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