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Both comments call attention to the inconclusive nature of i-PCR and report evidence that the authors made a fundamental error: Their PCR primer--the DNA fragment used to fish for a small sequence amid an ocean of genome--bound to other DNA sequences in addition to the target sequence, a common problem with PCR techniques.
The training and test datasets and a tutorial to calculate Tm for a small sequence manually are also provided.
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Since it is unachievable to assess all possible codon combinations representing a given amino acid sequence, it becomes clear from the aforesaid, that it is acceptable for many sequence features to reduce the search space by performing an exhaustive search for the best solution only inside a small sequence window, which is moved along the whole reading frame.
This genomic region has been sequenced almost to entirety with a small sequence gap, for which no genomic clones are available.
The sequence analysis of the Northern shrimp nuclease 1 kbp gene fragment was used to design primers for both 3'- and 5'- RACE, creating a small sequence overlap in the two fragments to be generated.
This provided a low yield product which was amplified for a smaller sequence (627 bp) with nested primer D1 [ 8], which contains standard sequencing primer sites.
In this way, DESIRE simulates actual biological experiments conducted for a smaller sequencing depth.
First, the techniques Chaos Game Representation, CGR [ 1, 3], and its bidirectional generalization by Universal Sequence Map, USM [ 14], will be revisited and illustrated for a small nucleotide sequence.
We note that some of the predicted gene structures are still incomplete and a search for small sequence stretches is notoriously difficult if one allows for variations.
For each small sequence segment, there are only a few more likely substructures.
We observed a false negative rate of 12.5% for small sequence differences and 25% for IS-element insertions.
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