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It is currently problematic to use circumchromosomal sequence data to develop an unambiguous emergence topology for E. coli.
The highly polymorphic control region (CR) was consistently problematic to amplify or sequence, resulting in parts of the CR missing for most species as well as flanking tRNA-Thr and -Pro for some species.
Due to the short nature of the reads used in DGE compared to other sequencing protocols it is problematic to correct for SNPs or sequencing errors by allowing mismatched bases.
Since there are two different signals that contribute to the observed average motifs, from OMP class and from taxonomy, it is problematic to use averaged motifs or sequence logos to determine the compatibility of a given protein-organism pair.
Indeed, excessive reliance on collinearity with the genome of A. thaliana may prove problematic for the ongoing efforts to sequence the B. rapa genome.
These repeated sequences can be problematic by complicating sequence verification via routine sequencing technology and could also lead to unwanted partial gene deletion via homologous recombination.
The ratio was well preserved through the initial amplification and after post-processing filtering to exclude problematic sequences and to trim error-prone ends.
Attaching elements of the genome to a particular location is problematic in sequence annotation, as exact coordinate locations will always vary between individual members of a species.
The 3' sequencing was more problematic than the 5' sequencing due to termination of the sequencing reactions at some of the long polyA tails characteristic of soybean and many other plant cDNAs.
The native cipA sequence has large repeated regions likely to be problematic for sequencing as well as genetic stability once introduced into T. saccharolyticum.
The protocol was designed to reduce the possibility that the data set contained unreliable sequences due to over-amplification of specific viral variants, problematic sequences due to PCR contamination, sample mislabeling, inter-subject contamination, intra-subject contamination or sequences that clustered with significant variance over independent samplings in a phylogenetic tree.
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CEO of Professional Science Editing for Scientists @ prosciediting.com