Sentence examples for motif finding algorithms from inspiring English sources

We also used motif finding algorithms to find potential consensus site for single base pair substitutions.

A widely used model is to cluster genes based on their expression profile and then using motif finding algorithms [ 7- 14] or motif enumerators to find the over-represented sequences within each cluster [ 15- 18].

First and most importantly, PSO+ differs from other motif finding algorithms by explicitly modeling gaps, which provides an easy solution to find gapped motifs.

PSO-EM simply uses PSO to find candidate motifs, which are then used as seeds by other expectation-maximization based motif finding algorithms, such as MEME [ 2].

Many motif finding algorithms, for example references [4] [15], have been developed and the performance of motif finding algorithms has been steadily improving.

Probability model-based de novo motif finding algorithms like MEME can be sensitive [59], [60], but may be too slow when thousands to tens of thousands of enriched regions need to be analyzed.

First, when using long DNA sequences, the computations of the motif finding algorithm MEME take too much time.

TRANSMODIS is not a motif finding algorithm rather it focuses on determining direct targets of a TF.

We used the motif finding algorithm MEME, to search exonic or intronic RNA fragments for over represented sequences [20], [21].

Search for over-represented sequence elements in 5'UTR and 3'UTR regions was performed using an enumerative Markov chain motif finding algorithm [68], which applies z-scores to evaluate the over-representation of exact DNA words, and SiteDB program [69].

Cawley et al. [ 60] note that the motif finding algorithm MDscan [ 22] recovers the known Sp1 binding motif from their data.