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For maintaining "housekeeping" functions across different cell types, for example, it would seem to be much less expensive to use the genomic sequence instead of complicated and error-prone gene regulatory networks.
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By using the genomic sequence of several related genomes, it is possible to infer how conserved a potential binding sites is, and thus to have a higher confidence in the conserved predicted sites versus the non-conserved sites [3].
Using the genomic sequence of CiLV-C, specific primers and probe were designed and synthesized to amplify a 73 nt amplicon from the movement protein (MP) gene.
Moreover, it has been found that budding yeast nucleosome occupancies measured in vivo by deep sequencing are accurately predictable using the genomic sequence only, indicating that the DNA sequence plays a major role in positioning nucleosomes in vivo [23].
In this study, we employed a systematic peptide identification strategy in which spectra derived from one organism were searched against the genome sequences of progressively more genetically distant neighbor organisms to measure the extent to which proteomic information could be obtained about one species when using the genomic sequence of another.
To identify gene order in other species, we used the genomic sequence when available.
The fraction of each of four deoxyribonucleotide moieties was determined using the genomic sequence of the bacterium.
Contigs were sorted using Mauve [ 43] and concatenated using the genomic sequence of C. ulcerans 809 [ 34] as reference.
To restrict the analysis to encoded motifs, we used the genomic sequence corresponding to each mapped read.
Amplifying primers were designed using the genomic sequence for each gene [ 9] in conjunction with Primer3 software [ 10].
An alignment was produced using the genomic sequence encompassing the rat promoter region with upstream purine-rich BSF1 element repeats, and homologous human and mouse sequences.
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