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The DsrC genes were re-analyzed and compared to both microbial sequences and the new viral DsrC from the Anantharaman et al. study.
After removal of ambiguous nucleotides, low-quality sequences (Phred quality scores <20), contaminated microbial sequences and ribosomal RNA sequences, a total of 265,294,865 cleaned reads (86%%) were harvested for further analysis.
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After identification and removal of human reads, microbial sequences were quality filtered and trimmed.
Various universal primers amplified both plant and microbial sequences, with different primers revealing different patterns of fungal diversity.
Non-human RNA sequences were subjected to a microbial discovery bioinformatics platform, and microbial sequences were analyzed by Metastats for association with KD.
Following the cross_match and trim2 processing, the sequences were further trimmed using Perl scripts designed in-house to eliminate known invalid sequences (e.g. microbial sequences, simple sequence repeats) and trim polyA/T tails, if present in a given sequence.
In P-DUDES domains of SRPX/SRPX2 and all microbial sequences, this region is short (approx. 10-20 residues) and in some marine metagenomic P-DUDES proteins it is missing altogether.
4. The sequencing done, computational techniques developed at Columbia University weed out human sequences and assemble the remaining microbial sequences to create the "fingerprint" of the mystery microbe. 5. Bioinformatics software compares the microbial fingerprint against databases of known microbial sequences, searching for close matches.
DNA microarrays are able to detect microbial sequences from any sample in a parallel and very fast, high throughput way.
These experimental tags were linked to the microbial virtual tag library, and only tags matching microbial sequences perfectly were further considered.
Larose, C. et al. Microbial sequences retrieved from environmental samples from seasonal Arctic snow and meltwater from Svalbard, Norway.
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