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Because of the relatively large number of samples analysed in our study we sought to minimise the sequencing of identical clones by screening with RFLP analysis, and sequencing a single representative clone from each RFLP group.
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To minimise the contribution of sequencing error to the distance between two sequences, jMOTU only counts mismatches between nucleotides, ignoring positions where one sequence has a gap or an undetermined base.
In this study, we have tried to minimise the effect of sequence error by preferentially using validated gene sequences when available and high quality genome sequence when not.
If scaffolds from both chromosomes can reliably be identified and filtered out then an optimal sequencing strategy would minimise the combined cost of sequencing and library construction.
This distinction is a further incentive to minimise the occurrence of sequence gaps.
In 19,114 of the SNPs detected by GigaBayes, each variant was present in at least 2 sequencing reads, minimising the impact of sequencing errors [ 33].
In addition, a systematic analysis of the transfer vector sequence was undertaken to minimise the amount of HIV-1 sequence within the vector and to remove signals that adversely impact on the processing of the viral genomic RNA (gRNA).
We refined this measure to minimise the influence of repetitive sequences and erroneous gene models.
We next employed Gblocks [ 101, 102] to minimise the impact of multiple sequence alignment errors and divergent regions.
Rather than looking for exact matches, Taxonerator uses the most similar existing sequences to annotate a MOTU, which minimises the effect of sequencing error on taxonomic conclusions, and allows accurate taxonomic placement of true novel taxa.
Preclustering reduces redundancy in the input sequence set and minimises the numbers of sequences that are involved in subsequent steps.
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