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Finally, any predicted protein whose sequence was either a subsequence or an identical duplicate of one entry in the RefSeq database was removed before conducting the database searches.
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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.
To exclude the possibility of drug resistance mutations impacting on the entropy calculations, epitopes containing amino acid positions known to acquire mutations causing high, intermediate or low level resistance to RT and protease inhibitors (Stanford University Drug Resistance database) were removed from the list of epitopes and all the calculations were repeated.
Duplicate articles within each database were removed, leaving 446 articles.
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.
To avoid redundant miRNAs, duplicated miRNAs shared between different species within the database were removed.
Contaminating sequences with very strong (95%) similarity with vector or any other sequence database were removed prior to clustering.
Potential chimeric sequences in this database were removed with DECIPHER [ 44] and UCHIME [ 45] [searched against the 2011 Greengenes database [ 46]].
First, 70 samples with array results inconsistent with the phenotypic database were removed (inconsistent sex based on chr X and chr Y probe sets).
The redundant sequences from cog0613 obtained from the NCBI database were removed using Jalview version 2.7 and then converted into FASTA format.
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