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Epitope peptides corresponding to original and modified sequences were validated in HLA binding assays and in immunizations of hemophilic E16 mice, DR3 and DR4 mice and DR3 × E16 mice.
The primers for modified sequences were: sense: 5'-TTGATTATTTGGTGGTGTGTGAG-3' (gi:37704377, 832-854) and biotinylated antisense: 5'-TCATCCATCTTACCTCCCTAATTT 3'-TCATCCATCTTACCTCCCTAATTT 3
Further investigation of the mature miRNAs at positions +1 to +18 (excluding the 3'-variable sequences) revealed that, although not predominant (∼5%), modified sequences were present in almost all the miRNAs.
While potassium adducts were also found to interfere in select instances, the potential overlaps between unmodified digestion products with potassium and modified sequences were determined to be significant enough to warrant not adding potassium adducts to the exclusion list.
The signature of the different sequences – the reference sequence and the whole set of modified sequences – were calculated and compared by Euclidian metric in order to obtain distances to the reference.
All sRNAs sequences from 18nt to 30nt obtained were removed from the vector sequences, then the modified sequences were further subjected to removal of rRNA, tRNA, snRNA, snoRNA and those containing the polyA tails, and finally the remaining sequences were compared against known plant Vvi-miRNAs in the miRBase [ 33].
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The modified sequences are searched by rps-BLAST against the "seed" domain sequence and the percentages of coverage are plotted against each amino acid position.
The cleaved or modified sequences are traditionally separated on a sequencing gel to determine the positions of more or less accessible nucleotides.
To analyse this region of the gene for methylation, PCR primers specific for the bisulfite modified sequence were designed.
Mutagenesis studies of OR5.24 revealed inversion from positive to negative charge selectivity by some point mutations [ 79], the resulting modified sequence is present in related receptors suggesting they are candidate ORs for charged amino acid olfaction.
Base modifications of the H. pylori UM032 genome were analysed, modified sequence motifs were determined, and the MTase responsible for each motif was deduced through a combination of prediction and characterization of cloned and isolated MTases.
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