Sentence examples for motif based approach from inspiring English sources

First of all, the sequences were separated that could be correctly predicted via motif based approach and the remaining sequences were then predicted using SVM.

[13] developed a phylogenetic conservation and motif based approach to predict tissue specific enhancers, which allowed them to annotate ∼5,500 high-confidence mouse tissue-specific enhancers for 61 murine tissue types by integrating tissue-specific expression data, conservation information, and cis-regulatory motifs.

Sequence, domain, and motif structure based approaches form the basis of Bayesian network models [ 36].

While most approaches focus on the disorder property, Stein et al. took a structure based approach focusing on the fact that most motifs that are found in disordered regions will take defined structure(s) upon binding [ 88].

In cross validation for hybrid approach, the results of motifs were directly added in the five or ten fold cross validation through SVM based approach.

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We selected RED, as this clustering-free approach has both recently been applied to P. falciparum and shown to detect motifs that clustering based approaches did not.

Furthermore, we also analyzed the significance of several selected network properties (Methods in Additional file 1) for each type of regulatory motif based on similar approaches adopted in the PPI enrichment analysis.

The Pax8 binding motif here defined encompasses motifs obtained by individual-gene based approaches, such as those defined for rat and human TPO[ 9, 12] and for the rat Nis upstream enhancer [ 7], as well as those defined by in vitro studies outlining the binding sequence for Pax8 [ 13] and the Pax2/5/8 subfamily (AAGCGTGAC) [ 14].

In contrast, k-mer based approaches use a word-based sequence of length k to enumerate possible instances of a motif.

Compared to PWM-based approaches, the k-mer based approaches can be designed to make fewer assumptions about the degree of TFBS degeneracy, length of the binding sites, and position dependences of a motif.