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To understand the solution to this dilemma, it pays to examine sequences: an important aspect of pattern application that is often overlooked.
The information entropy methodology for analysis of protein variability was modified to examine sequences of 9 amino acids or longer, instead of the more common application to single residues, as a means to relate the conserved sequences to the immune function of HLA-restricted peptides.
Although ω provides a convenient and commonly used method to examine evolutionary constraints, it has typically been used to examine sequences that have diverged relatively recently.
Dynamic programming is used to search for similarity (local or global), to generate a multisequence representation (profile), and to examine sequences with hidden Markov models.
For unicellular eukaryotes, much of the data has not been reviewed and the researcher needs to critically examine sequences to verify the quality.
To examine whether motifs predicted by iTriplet had biological activity, we chose to examine sequences important in the 3' end processing of mammalian pre-mRNA, in particular sequences found just downstream of the cleavage and polyadenylation site.
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Algorithms may examine local sequence effect on site accessibility, or examine sequence content for particular nucleotides [27], [30], [33].
To examine sequence conservation across the 2 kb 5' flanking regions, a TCOFFEE multiple sequence alignment was prepared (Figure S1).
To examine sequence relationships within the KAP-β family across the eukaryotes, we performed a semi-automated search of a panel of predicted proteomes.
To examine sequencing accuracy, TA cloning was performed.
To examine sequencing variations, cDNA library replicates of each condition were constructed.
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