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To avoid redundant miRNAs, duplicated miRNAs shared between different species within the database were removed.
Third, 16S reads containing possible chimaeric sequences that had BLAST match lengths of < 90% with reference sequences in the database were removed.
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To further investigate the influence of this factor, we have performed two different tests: a deletion experiment, in which a percentage of the database is removed to simulate a reduction in our current knowledge, and a test of assignment involving sequences from rare taxa, which probably represent the most serious challenge to the method.
Protein sequences derived from genes annotated as pseudogenes in the databases were removed after the initial screen (see materials and methods for details).
Short sequences that matched only one of the Bet v 1 fragment HMMs provided by the Pfam database were removed from the list.
Those ORFs with a top BLAST hit to a non-methanogen or with no homology to the nr database were removed from the analysis, as were transposase sequences (which are unlikely to represent good vaccine targets), while adhesin-like ORFs are dealt with separately above.
Probes from uncertain chromosomal loci (Chr -random, Chr -randomm, chrE22C19W28_E50C23, chrE64, and W chrE22C19W28_E50C23chrE64tandse) Were removed from the results.
The redundant sequences from cog0613 obtained from the NCBI database were removed using Jalview version 2.7 and then converted into FASTA format.
Further sequences matching non-coding rRNA, tRNA, snRNA and snoRNA in the Rfam database were removed.
Sequences matching noncoding rRNA, tRNA, snRNA and snoRNA in the Rfam database were removed.
First, 70 samples with array results inconsistent with the phenotypic database were removed (inconsistent sex based on chr X and chr Y probe sets).
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