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Genes were identified in EST and genome trace archives based on similarity to vertebrate sequences.
Mining of NCBI trace archives: TAAR sequences of various mammalian species were obtained by using the respective mouse ortholog nucleotide sequences as query sequence in discontiguous megablast and blasting all available mammalian trace archives.
Of the 2,027 non-primate trace archives, 454 (22.39%) were identified as contaminated with human sequence (Table S1B).
Many Alu sequences were found in the Trace archives for species from all phyla (Figure 1A D, Table S1A B).
Candidate YSNPs were chosen on the basis of appearing in only the above reference contigs and none of the traces in the Trace Archives.
We confirmed these features by inspecting the corresponding trace archives.
Multiple frameshift mutations in Choloepus AMEL are confirmed by Trace Archives chromatograms (Additional file 8).
All of the inactivating mutations in Choloepus are corroborated by chromatograms in NCBI's Trace Archives.
The TblastN hits from the genomic trace archives were validated and grouped using subsequent blast analyses.
Interestingly, this haplotype is also found in the trace archives of chimpanzee and baboon.
Comparisons with the trace archives suggest that these are all genuine mutations.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com