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LabB1 is created by corrupting a clean sequence heavily using the relation G x) = (1 - α(x))I x).
The recovery from the acrymalide gel and the reamplification were tricky steps and thus we were not able to get a clean sequence for all cDNA fragments.
That these were double infections was ascertained through the observation of a clean sequence using primer pairs that distinguish clades within Wolbachia, making a total of 33 strains detected.
Here, we report statistics on primer combinations that consistently yielded a single band and whose product generated a clean sequence in at least 70% of taxa tested (five loci), as well as sequences for a few primer sets that could be of utility with additional optimization or in a different subset of taxa (Tables 1 and 2).
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The number of these fixed and movable artifacts can be reduced by a clean sequencing set-up and the steps described above.
We defined the k-mer length as 17 bp; thus, a L bp-long clean sequence would include (L-17 + 1) k-mers.
A total of 143010 unique transcripts (UTs) were predicted from the clean sequence reads, with an average length of 1482 bps and an N50 of 1155 bps.
Prior to mapping these tag sequences to reference sequences adaptor tags, low quality tags and tags of copy number = 1 were filtered, producing an average of 5.6 million clean sequence tags per library, with 169,997 distinct clean tag sequences.
Two of the PCR products (M. albescens and M. horsfieldii) for the intergenic region failed to yield clean sequence so an additional intergenic primer was used.
From the array data, calls could be made for ∼97.5% of the bases, and false positive rates were very low with only a single mutation reported from the array dataset for which the corresponding dideoxy trace had a clean wildtype sequence.
For P. gangelion, we failed to amplify a clean COI sequence with the degenerate primers used for the other species.
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