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Both vector and low quality sequences were trimmed off the original sequences.
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The electropherogram sequencing files were processed using the Phred program [46] for base calling and for trimming of vector and low quality (<20) sequences.
Unknown vector and low complexity masking was performed by SeqClean.
After trimming vector and low quality sequences the average PHRED 20 read length was 693 bp.
Following removal of vector and low quality sequences, all sequences ≤ 50 bp in length were discarded.
Base calling was performed using TraceTuner and sequences were trimmed for vector and low quality sequences using Lucy [ 25].
Briefly, primer, vector and low quality sequences were removed at the 5' and 3' ends of each sequence using Cap3 and Phred software [ 54- 56].
We sequenced the 5'- or 3'-end of 85,721 clones, yielding 63,395 and 22,326 sequences of 5'- and 3'-ESTs, respectively, after filtering the vector and low quality sequences.
After sequence processing and removing vector and low quality sequences, a total of 4,594 high quality reads (2,455 5 ' end and 2,139 3 endnd) were obtained (Table 1).
The sequences and quality files from trace files were read by the Phred program for base calling and trimmed to remove vector and low quality bases [ 28, 29].
Sorghum genomic reads (593,969) were downloaded from NCBI and processed using the Lucy program [ 50] to remove vector and low quality sequences.
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