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Inherent conflicts among individual gene trees are further exacerbated at the scale of whole genomes by inaccurate or incomplete annotation of many sequences, as well as the potential for external contamination, when incompletely assembled genomes or EST databases are run through automated pipelines.
Prudence suggests that the researcher needs to evaluate as many sequences as available for designing species-specific PCR primers.
Since high-throughput sequencing of partial 16S rRNA genes is becoming both more common and larger in scale, an approach targeted at classifying as many sequences as possible to species-level would be useful.
In the second approach, alignment subdivision, the missing data is statistically modelled in order to retain as many sequences as possible in the phylogenetic analysis.
Given a set of sequences, it searches for motifs that occur (with a bounded number of mismatches) in as many sequences as possible.
SSPACE is a stand-alone scaffolding tool, which we implement using the un-normalized input data to provide as many sequences as possible for assembly correction and expansion.
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Consequently, a single 8 point, black-on-white, ambiguity symbol can convey the presence of two, three or four different nucleotides in this particular position for as many DNA sequences as are being compared.
Screening of the CVa2X and CCa2X libraries with Rattus norvegicus PFTase revealed reaction by many known recognition sequences as well as numerous unknown ones.
Frodo's quest is the main focus, and Aragorn is the main sub-plot, and many sequences (such as Tom Bombadil) that do not contribute directly to those two plots were left out.
Among many sequences identified as A-rich sequences, AAUAAA is the most well-conserved sequence in both yeast and plants.
Comparison of data from individual sequences after binning the PrePS scores into low, medium, and high values shows that many sequences observed as positives in the library screening are predicted to be PFTase substrates by PrePS.
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