Sentence examples for motif model using from inspiring English sources

The SWISS protein database was searched with the FoxD3 eh1-like motif model using an E-value threshold of <104 for reported sequences.

These models extend the popular PWM motif models used in computational biology to represent and identify sequence features such as TF binding sites (TFBSs), splice junctions and binding domains in DNA, RNA and protein molecules, respectively (GuhaThakurta, 2006; Stormo, 2000).

Using IUPAC strings as motif model and using the MapReduce programming model to enable distributed computing, it was shown that it is feasible to compute all genome-wide conserved words in a large dataset in an exhaustive manner.

> -wrap-foot> Table 3 compares the proposed method with a state-of-the-art by 5-fold cross-validation on the 12 variants of human poly(A) motifs: the RF model using domain-specific features by Kalkatawi et al. (2012).

Our model, using motif scanning and HAc local minima, improves the sensitivity for TF binding site prediction by ∼50% over a model based on motif scanning alone, at a false positive rate cutoff of 0.01.

To evaluate the potential for simultaneous binding of three proteins (ETS monomer and CREB dimer) to the ETS⇔CRE motif, we built a molecular model using PDB files of the ETS1 protein bound to an ETS site (PDB ID: 1K79) (Garvie et al. 2001) and the CREB dimer bound to the CRE (PDB ID: 1DH3) (Schumacher et al. 2000).

Fan et al. [2] identified SNP-containing regulatory motifs in the myelodysplastic syndromes model using data from SNP and gene expression arrays.

The correlation coefficient of the model using this random motif and the primary factor will be estimated.

We propose DISCOVER, a discriminative model using CRFs for motif discovery.

We then rebuilt a new SVM model using the remaining motifs, and tested its accuracy on the test set.

The resulting RNA motif model was used to scan the complete genomic sequences of 10 different lentiviruses, as well as the recently identified rabbit endogenous lentivirus type K (RELIK) (see Materials and Methods).