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Finally, we performed a location analysis of the M1 and M11 matches in the human genome and found that 80% of the matches were at ZNF genes; for M1: 569 of 724 top matches and 968 of 1198 lower stringency matches; for M11: 148 of 190 top matches and 571 of 703 lower stringency matches.
The software was set to identify high stringency matches and the resulting data manually curated using the high throughput results viewer interface of HT-GO-GAT.
If the second alignment was found, the clone was presumed to be non-chimeric, with the lower-stringency match reflecting either nuclear-incorporated organelle DNA or sequencing error in the organelle sequence.
Any sequence that had 20 or more high-stringency matches in the reference genome was considered repetitive.
Designing a COS involves decisions regarding stringency of match, order of comparisons, and definitions of orthologs [ 14, 17].
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%).
To further increase stringency, reads matching wheat miRBase entries were filtered out [ 39].
While we may miss some alignments involving rare non-standard introns or some Agilent cDNA clones due to our algorithm, we maintain a high stringency of matches between genome coordinates, probes, and transcripts.
Because of the stringency of the matching algorithm employed, matching proved impossible for most patients receiving vasopressors.
As L and S increase, so does the stringency of the match.
Therefore the 26/26 (perfect match) stringency rule was maintained in this analysis to ensure a less ambiguous annotation of differentially expressed tags.
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