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A method will contain a sequence of instructions to be executed by the program.
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Since most prokaryotic genomes are organized in operons, the first gene of the operon will contain a leader sequence while the subsequent genes within that operon will be leaderless.
This is because a cluster seeded with a chimera (composed of genes A and B, say) will contain a mix of sequences from genes A to B. This chimera-seeded cluster, depending on the value of k, would be able to merge with both clusters containing A sequences, and clusters containing B sequences.
Energetically active tissue (such as muscle) should be avoided, as there is a risk that the sequence data will contain a high proportion of mitochondrial DNA (mtDNA), which wastes sequencing effort and can cause problems in the assembly step due to the extreme read depth (as assembly pipelines often use read depth to identify duplicated genomic regions).
If hosts belong to different species, the resulting sequencing electropherogram will contain a variable number of ambiguities (i.e. double peaks).
For example, if a child has a heterozygous site but only one parent's DNA was captured by the exome sequencing protocol, that site will appear to contain a sequence not found in either parent.
Since the 114 nt mean fragment length is less than twice the 75 nt read length, in most cases the pair of reads simulated from a fragment will contain overlapping sequence.
Such tags will contain adaptor sequence that prevents mapping to the genome.
It therefore seems reasonable to expect that regions close to the TSS will contain functional sequence motifs involved in transcriptional activation of OR genes.
An effective measure zero set of sequences will contain sequences which can be effectively determined to have a 'special hallmark' (for example, having a '1' at every seventh place, or never having the string '000000' occurring as a subsequence).
At this error rate up to one-third of the 33 bp DG sequences will contain sequencing errors.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com