In particular, clones aSP-a, aSP-f, aSP-h, and pMP-e have extensive arborizations in the MERs that are absent from females.
This fragment is found in SCC mer that is associated with SCC mec type III.
As a concrete example, consider a k-mer that is present in all samples with a similar abundance.
Next, we transform each read cluster to a contig by first identifying a k mer that is shared among all reads, then generate alignment of these reads by directly matching this k mer.
This microarray has long oligonucleotide probes (60 mer) that were in-situ synthesized onto glass slides using Agilent SurePrint technology and has been developed into an 8X15K format (8 identical arrays on a single slide).
Transportan, MPG and Pep-1 are chimeric peptides (∼30-mers) that are formed by the fusion of two natural sequences derived from galanin/mastoparan, HIV-gp41/SV40 T-antigen and HIV-reverse transcriptase/SV40 T-antigen, respectively.
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Peptides that were recognized had a significantly lower degree of similarity to human proteins than the 10-mers that were not reactive.
Again, deviation from this expected outcome suggests possible biases in the reads, allowing one to identify k-mers that are biased towards appearing at specific positions.
The conservation score measures the fractions of 7-mers that are better conserved than the motif, i.e. a conservation score of 1 means that the motif is better conserved than all 7-mers.
