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Moreover, close homologues have already been eliminated by sequence analysis earlier.
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The second possibility is that intron losses that change coding sequences have essentially been eliminated by purifying selection.
Off-target effects were eliminated by Sanger sequencing.
The important feature of the SAC-OCDMA systems is that multiple access interference (MAI) can be eliminated by code sequences of a fixed in-phase cross-correlation value.
Thus, the risk of introducing untargeted mutations cannot be eliminated by batch sequencing the population of fragments derived from a single PCR.
Finally, trivial redundancy was eliminated by discarding sequences with identical values for size, GC1, GC2, and GC3 (or a difference of GC3 <2%).
Splice variants, polymorphism and duplicates were eliminated by applying 90% sequence identity cut-off using CD-hit [ 42] and also checked manually.
Sequence duplicates due to PCR amplification were eliminated by removing identical sequences linked to the same random barcode primer.
Interspersed repeat sequences within the downloaded DNA sequence were eliminated by RepeatMasker (http:// www.genome.ucsc.edu) and the repeat masked genomic sequences were analyzed using NCBI BLAST2 (http://www.ncbi.nlm.nih.gov/blast/bl2seq/bl2.html).nih.gov/blast/bl2seq/bl2.html
The possibility that these were intronless retroposed copies was eliminated by the amplification and sequencing of intron-containing PCR products from each BAC clone, demonstrating that the sequence of these products was identical to that of the original probes.
There may be a specific mechanism for transcription initiation that omits the signal peptide sequence, or this sequence might be eliminated by the action of an RNA exonuclease.
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