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Control samples were analysed with each series of routine samples, results plotted in the software and tested for alignment.
2. Probes without exact matches are then tested for alignment with single base pair mismatches, again using a hash table approach with an expanded dictionary to include all possible mismatch sequences.
Further, the short k-mer length causes Trinity to run considerably more slowly than Oases run with 67-mer, since more words of size k per read have to be constructed and tested for alignment.
Similar(57)
Dayhoff's (PAM) matrix was also tested for each alignment, but the results were essentially the same (not shown).
The 469SBP and 469CT topologies were tested for all alignments (see methods).
Prior to each experiment, the confocal microscope was tested for field illumination alignment, optical efficiency, colocalization, and axial resolution (Lerner and Zucker 2004; Zucker 2006a, 2006b; Zucker and Lerner 2005; Zucker et al. 2007); and the lens was inspected and cleaned before use.
Similarly, each pred-CA sequence was considered has having no representative in the tested dataset for alignment spanning less than 100nt or having less than 98% identity.
We tested for both forms of alignment using a set of 10 independent populations of Drosophila melanogaster that were adapted to one of two environments.
All primers were tested for specificity by sequence alignment in the PubMed nucleic acid database (http://blast.ncbi.nlm.nih.gov/Blast.cgi).nih.gov/Blast.cgi
Primers were designed using Primer Express software v1.5 [ 38] (Applied Biosystems, Foster City, CA) and tested for their specificity by alignment using the BLASTN program, followed by dissociation curve and primer efficiency tests.
Figure 1 illustrates the alignments tested for each technical sequence.
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