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Exact(8)

To avoid spurious joining, datasets with many unique sequences required longer overlaps than those with few unique sequences (Figure 4A).

The low depth of coverage and short length of 454 sequence reads have also created new challenges for probe design, i.e., too many unique sequences (both contigs and singletons).

The majority of the clusters (55%) are individual sequences (Table 4), strengthening the observation that there are many unique sequences that do not share even a common sub-sequence with other proteins and that the predicted protein datasets provide remarkably different alternatives.

The numbers of identical sequence groups with a sequence from one (22,556 groups), two (2,058), three (521), or all four (101) prediction methods confirms the observation that the gene prediction methods produce very different results, with many unique sequences for each prediction method.

Generally, A. thaliana has a relatively compact genome and contains many unique sequences, e.g., 64.5% singletons by our definition in which 6.78% of P/A genes were identified.

While some of the unique sequences are similar to housekeeping genes, many unique sequences are similar to genes that may influence stridulation (Table 4).

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Similar(52)

If the starting data include many more unique sequences than this (>10,000) we recommend preclustering in batches, and combining preclustered sequences for a complete analysis (see the jMOTU user guide for details).

Many unique mutated peptide sequences fitting to the patients HLA-haplotype were identified.

The median ORF size was 225 nucleotides (range 102-1,464) suggesthat that many of the unique sequences have the potential to encode proteins.

Given that our data show many unique V1R strep sequences for Microcebus, in addition to those culled from the low-coverage Trace Archive Microcebus genome by Young et al. (2010), it is likely that V1R repertoire diversity has been significantly underestimated.

The C. elegans genome encodes approximately 30,000 piRNAs, many of which map to unique sequences in two broad clusters on a single chromosome, and are not generally associated with protein coding regions or genes [ 84- 87].

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