Sentence examples for motif identification algorithms from inspiring English sources

This is particularly important for analyses of candidate transcription factor binding sites, for which the core motifs are under 10 nucleotides long, and which tend to be over-predicted by motif identification algorithms.

This discrepancy highlights the difficulty of choosing appropriate parameters for motif identification algorithms.

It is typically approached by position weight matrix-based motif identification algorithms using Gibbs sampling, or heuristics to extend seed oligos.

We previously used a combination of microarray analysis and a motif identification algorithm to identify 46 potential Zap1 targets [ 3].

That study used genome-wide transcription profiling with DNA microarrays coupled with a motif identification algorithm, MEME.

In this current study, we have further characterized the Zap1 regulon using additional microarray experiments and a more sensitive motif identification algorithm.

Therefore, we analyzed the promoters of the 53 candidate genes (Fig. 1A) using a more sensitive motif identification algorithm called Regulatory Sequence Analysis Tools or RSAT.

With alternative growth conditions for the microarray experiments and a more sensitive motif identification algorithm, we identified 31 new potential targets of Zap1 activation.

Furthermore, despite progress having been made identifying key sequence motifs within vertebrate promoter elements [ 22], ancient CNEs have remained somewhat recalcitrant to systematic motif-identification algorithms, despite some elegant targeted approaches.

We also used a smaller dataset consisting of evolutionarily conserved promoter subregions as input to MEME, because ab initio motif-identification algorithms like MEME should do better on input datasets that are more enriched in true functional elements.

However, our complementary analysis using the ab initio motif-identification algorithm MEME revealed a very similar set of enriched motifs as we found using the MatBase database as a starting point.