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The primary filters include a threshold for minimum observed frequencies for each word in both sequencing directions and a cross-verification of the sequence through partial assembly of words from independent sets of reads.
For nuclear loci, heterozygous individuals were verified by the presence of two similarly sized, overlapping peaks observed in both sequencing directions, and were coded using standard IUPAC ambiguity codes.
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The overall rates of these substitutions show symmetry in both sequence direction and between complementary nt changes.
To call a mutation we adopted the standard practice that it should be observed in at least two independent PCR reactions (avoiding possible PCR misincorporation due to Taq polymerase infidelity) and in both sequencing directions (avoiding sequencing anomalies due to misincorporation of dideoxy terminators).
Primers flanking one recognition sequence allowed sequencing from both directions, and the resulting sequences were aligned with pUC19 (Figure 4).
The seven loci were sequenced in both directions, and sequence data were checked manually for positions of homozygotic or heterozygotic polymorphisms.
The 5'UTR region of all the 201 untypable isolates were sequenced in both directions and sequences that were obtained for the first time were submitted to GenBank data base.
These amplicons were sequenced in both directions and the sequences were then assembled and shown to include a single large open reading frame as expected.
Positive clones were selected to sequence in both directions and each sequenced twice independently.
The resulting amplicons were again sequenced in both directions, and the sequences were run through PlasmoDB BLAST and NCBI BLAST/n tools, with the exception of the Pvr47 amplicons.
Approximately 36,000 cDNA clones (average insert size of 800 bp) were sequenced from both directions and after sequence quality assessment a total of 50,248 ESTs were collected.
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