The parameters of the HMM can be initialised by using a single sequence or a pre-existing alignment.
Using a single sequence for each OTU, evolutionary distances were calculated with the Jukes-Cantor (tree-Markov) model and phlyogenetic trees determined by the Neighbour-Joining method, with 1000 trees generated.
This suggests that using information from multiple MRI sequences to characterise BMLs may provide more prognostic information than using a single sequence alone.
Primers were designed based on simultaneous viewing of the Se-Al file and an Oligo 4.02 (Rychlik, 2002) file, using a single sequence from the pool.
Given heterozygous nucleotide sites in β-globin, data analyses were conducted on inferred haplotype states rather than using a single sequence with ambiguous nucleotide codes for heterozygous sites.
We have shown that a traditional mapping approach using a single sequence as reference is incapable of dealing with the great allelic differences of HLA genes, with a large number of sequencing reads being missed.
Second, using a single sequence would reduce the cost of production because synthesis, quality control and toxicology would be limited to one molecule, or a few in the case of using a combinatorial approach.
For computational efficiency, an initial scan was done using a single sequence, excluding families where the top hit had an e-value of 1 or greater to any protein of known structure.
On the other hand, since the use of two positive RNAi systems suggests that Wang et al. were aware of the potential weaknesses of the system, this raises the question as to why they only used a single sequence for their RNAi control experiments.
Namely, RAF uses a single-sequence RNA secondary structure prediction program CONTRAfold; Do et al., 2006b) and a pairwise RNA sequence alignment program (CONTRAlign; Do et al., 2006a), respectively, to construct a constraint set 𝒞 of allowed base pairs and aligned positions in a and b.
Using a single sequencing primer, a total of 3 CpG dinucleotides were sequenced for each Satellite 1 element targeted.
