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To address this limitation we assess our model's performance using distance distributions between the predicted and true mature miRNAs for each precursor sequence, as detailed below.
RNA oligo markers (18-mer, 24-mer; sequence as detailed from [ 6]) were purchased from Dharmacon (Lafayette, CO) and 2' ends were deprotected prior to use as indicated by Dharmacon.
The independent researcher will then (i) consecutively number all participating practices in this group (ii) generate the random allocation sequence as detailed (iii) assign practice to group allocation and (iv) notify the PRINCE Project Manager of the practice allocations.
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PCR products were analyzed on 1.5% agarose gels in Tris-acetate/EDTA (TAE) buffer, extracted and sequenced as detailed above.
Due to the large size of exon 1, it was amplified at 95°C for 15', 35 cycles of 95°C 1' 30″, 65°C 30 sec, 72°C 2 min with a final extension of 72'C for 7 min. PCR products were checked on agarose gels, and then sequenced as detailed below.
The fosmid inserts were subjected to further characterization using functional analysis and whole insert sequencing, as detailed in the following.
The structured coalescent, allowing for serially sampled sequences as detailed by Ewing et al. (2004), assumes the following demographic model.
This freely available electronic tool facilitates the information-rich design of protein constructs and their engineered synthetic gene sequences, as detailed in the accompanying manuscript.
The alignment and comparison of paralog sequences as detailed in Katju and Lynch [ 35] enabled the identification of duplication termination points and the degree of structural resemblance between paralogous sequences.
The numbers p75-80 and p75-534 refer to the particular tumor bearing mice in the transgenic mouse cohort expressing the p75 CUX1 isoform under the control of MMTV regulatory sequences, as detailed in the introduction.
The 454 sequencing resulted in ten contigs ranging in size from 2 KB to 3.5 MB and harbored 236 gaps of ranging from 4 nucleotides to 2 kb in length which were closed by PCR amplicon sequencing as detailed in the PCR primer design and amplicon sequencing section.
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