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Sequencing of the spot produced a small fragment of protein similar to the mammalian nuclear ER.
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Sequencing of the spotting solution rather than the AFPs is possible only if the spotting solution solvent does not interfere with the sequencing reaction.
The three AKIP1 isoforms specifically bound clusters of sequences, shown in Fig. 4A, with the sequence of the spotted peptide shown to the right of the peptide spot.
Three mtDNA control region sequences of the spot-billed duck (Anas zonorhyncha) were retrieved from GenBank (accession numbers AY506945– and06947) and were included in the NJ tree analysis to discern their phylogenetic relationship to domestic samples.
However, peptide sequencing of the corresponding spot could not detect any modification (sequence coverage of 85,5%).
These observations would need to be confirmed by N-terminal sequencing of the different spots.
Peptide sequences of the protein spots were determined by BLAST and SEARCH against the NCBI website and the InterProScan database [ 6].
Perhaps most importantly, the RNA1 and 2 sequences of the chocolate-spot-associated virus were only ~80% identical with those of ToANV, ToMarV and ToTV.
For the correlation analysis of sequence identity and hybridization signal ratio, the sequences of the probes spotted on the A. palmata array were blasted against a M. faveolata transcriptome data set and orthologs were determined by using reciprocal tBLASTx [ 76].
A BLAST search with the complete nt sequence of the chocolate-spot-associated virus RNA1 revealed 74 and 69% identity with RNA1 sequences of ToMarV and ToTV, respectively, and 74% identity with the partial ToANV RNA1 sequence available in GenBank.
A BLAST search with the complete sequence of the chocolate-spot-associated virus RNA2 sequence revealed 76, 75 and 70% identities with those of ToMarV, ToANV (partial sequence) and ToTV, respectively.
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