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For example, simply having many redundant sequences rather than fewer diverse sequences is likely to negatively impact contact prediction, and one would like to choose the optimal input alignment for this process.
This initial dataset includes many redundant sequences identified simultaneously by two or more similarity/pattern searches.
Some sequences were readily available in GenBank and in helpful automated databases like Pfam (with many redundant sequences present) and Superfamily [ 21].
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Another interesting feature of piRNAs is that there are many redundant piRNA sequences, whereas the same does not appear to be true for CRISPRs.
This indicates that, in many cases, several redundant sequence entries from EST and genome databases were combined under one CLE number.
For eukaryotes, transcriptional regulation in is a much more complex issue, involving many redundant binding sites dispersed along genomic sequences.
Sequencing the positive clones revealed many redundant clones, and 45 independent clones were identified as candidate genes whose expression was more enriched in the OLs than in the other brain regions.
This approach allowed us not only to readily identify genes without tremendous sequencing works in the subtracted amplicons regardless of many redundant clones, but also to easily evaluate the subtraction efficiency and specificity.
This reported sequence count is not equivalent to a receptor count, as many of these sequences may represent fragments of a single protein or prove to be redundant sequences.
The remaining sequences were then pooled with WGS scaffolds together to extend and collapse redundant sequences.
Subsequently, each sequence containing the protein kinase domain was extracted, and redundant sequences were deleted.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com