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The MUC1*1110 expression construct was made by cloning in frame the sequence corresponding to the C-terminal 145 amino acids of MUC1 beginning at GTINV.and ending at.AAAASANL after the nucleotide sequence for the signal peptide.
Maximum likelihood heuristic searches were run after the nucleotide substitution model best fitting the data was selected by Modeltest v3.7 [ 65].
In addition to these two SNPs, a deletion of nine bp (three aa) was detected after the nucleotide at position 3348 bp (1113 aa) when compared to the porcine reference sequence [Ensemble: ENSSSCG00000016068].
Insertions are described by a '+' or a '-' after the nucleotide flanking the insertion site, followed by the position of the first inserted nucleotide of the intron (beginning of intron = +1, for insertions flanking the acceptor site: end of preceding intron = -1), followed by 'ins' and the length of the inserted sequence.
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After selecting the nucleotide variations with frequency equal to 100.00, we identified 252,343 SNPs and INDELs between BG23 and Nipponbare and 326,351 SNPs and INDELs between LG10 and Nipponbare.
After translating the nucleotide sequences we found variation in the length of the glutamine tract for ten of these genes.
After verifying the nucleotide sequence, the fragment was excised as a PstI– XbaI fragment and cloned into pMDC123.
Bayesian inference (BI) analysis was carried out in MrBayes 3.1.2 [ 32] after partitioning the nucleotide matrix according to genes.
The open reading frame of each gene was manually examined after translating the nucleotide sequences with the getorf module from the EMBOSS package [ 39], version 3.0 [ 40].
T bars are the expected frequencies with the optimized mixes (after rounding the nucleotide frequencies at the nearest 5%, see Methods).
To construct a consensus map, SNP loci were merged based on EST names after omitting the nucleotide position of the SNP within the name.
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