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Reads that were not assembled into contigs in the reference assembly were entered into a subsequent de novo assembly with a higher stringency minimum match similarity (90%).
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In BlastN analysis, a cutoff value of E-10 and a minimum match length of 100 bp with similarity threshold of ≥ 85% (for comparison with P. monodon ESTs) or ≥ 80% (for comparison with the ESTs of the other 3 penaeid species) were used.
In BlastX analysis, a cutoff value of 1 × 10-5 and a minimum match length of 300 bp were used as the similarity threshold.
All components from AMDIS analysis were searched in the NIST database (with one reported hit per compound and with a minimum match factor set to 60%, meaning that a threshold of 60% similarity was used for the spectral matching.
Figure 2 displays the queries associated with each of the predictors on the correct match similarity vs. best match similarity plane.
Figure 2 Contour plots on the best match vs. correct match similarity plane of the query distributions.
All chromatograms were matched against this reference chromatogram with a minimum match factor of 800.
Assembly parameters of 88% minimum match with 17 nt minimum overlap were used to define unique spacers and resulting contigs were spacer-spacer matches.
Cross-match was then used to mask vector sequence in each read (minimum match of 10, minimum score of 20).
Assembly for contigs was performed with match size of 50, minimum match percentage of 97, minimum sequence length of 100.
A maximum for the false match rate F' can be estimated using an anticipated minimum match rate.
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