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No polymorphism was detected in any sequences that have the same SSCP profile.
The proteome can be searched for any sequences that have experimental validation.
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A second filter was used to add additional sequences to the results of the first step, and any sequences that had not been identified in the first step were added to the set of results.
One would expect the denatured DNA to migrate differently to dsDNA and not give bands of expected restriction fragment sizes upon hybridization with the single copy probes, but any sequences that had fully resisted the denaturation treatments would give such bands.
Step 2 filters the dataset using an 80% similarity threshold to eliminate any sequence that has a similarity of 80% or greater with one or more sequences in the dataset.
Any sequence that had 20 or more high-stringency matches in the reference genome was considered repetitive.
Any sequence that has significantly higher score for one of the constructed PWMs is assigned to that group, whereas sequences with low scores or without pronounced preference of one PWM are assigned to the virtual group.
Of the 115 TDFs identified in Cluster C, 41 did not match any database sequences or matched sequences that have yet to be annotated.
For all other input formats, COUGER will start with Step 1, removing from each set the sequences that have an overlap with any sequence from the other set.
However, there are some peptide sequences that have no relationship with any positive or negative training sequences.
Under a given cluster threshold, these proteins represent the sequences that have not been grouped with any other sequence.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com