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To guarantee that every exact match of length w between a query and a subject is found, we use the relationship s= w− k+1.
Finally, for our heuristic we need to find for an index i all positions belonging to the respective other sequence, where a match of length s(i) occurs.
For example, in C. elegans a perfect match of length 30 in the middle of the oligonucleotide will introduce similar cross-hybridization noise as a perfect match of length 23 close to the slide or length 36 at the end away from the slide.
In fact, a perfect match of length 20 at the end away from the slide will produce a measurable fluorescence intensity above background so our standard elimination of non-unique 20 mers is justifiable in these instances.
We therefore settled on an intermediate BLAST E-value cutoff of 1e-3 for all non-miRNA families, which by observation corresponds to an exact sequence match of length 24.
The PSSM chaining problem for a single sequence S j can be considered a chaining problem for pairwise matches between sequence S j and a virtual sequence V[1.. L] such that a match for PSSM M i is a match of length one at position i in V.
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If this match of lengths is not possible, zero stuffing - the insertion of additional zeros into the DFT frame - can adjust the signal frame to the DFT frame.
It first finds all exact matches of length q between the query and subject sequences.
By default, TGICL requires exact matches of length 18 to identify candidate sequence pairs.
The representative indexing strategy is to construct indices based on exact matches of length k (k-mer).
Intuitively, there cannot be an approximate match of small edit distance between a read and the genome if not one or several exact matches of length q exist.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com