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As a first step, MarkerMiner filters each user-provided transcriptome assembly using a minimum length parameter.
By using a minimum length of 3 characters, gene and protein family names like 'p53' or 'WNT' are still regarded as valid items.
A database from our transcript data was constructed using TransDecoder [ 137], http://transdecoder.github.io, version r20131110), using a minimum length open reading frame of 5 amino acids or more than 10 nucleotides, as parameters.
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Because I chose to use a minimum length as the stopping condition, the shape of the tree depends on the size of its trunk.
We analyzed these low-quality reads, using a minimum intron length of 5 bp, a maximum intron length of 6 kbp, and an anchor size of 6 bp.
The input genomes are searched using Nucmer in an all-against-all manner using a minimum match length of 15 nucleotides and a cluster length of 60 (-l 15, -c 60).
To control for this effect, we also retrieved the 3 matches described above using a minimum alignment length cutoff of 98%, on the basis of the query sequence length.
Candidate constructions are evaluated using a minimum description length criterion that balances a structural bias toward simpler grammars against a data-driven bias toward more specific grammars.
K was deduced automatically using a minimum description length cost function.
These transcriptomic libraries were assembled from reads using a minimum overlap length of 40 bp and a minimum overlap identity of 98%.
The final de novo assembly was constructed using a minimum overlap length of 45 nt, minimum overlap identity of 96%, and an alignment difference score of −6.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com