Sentence examples for based on position matrix from inspiring English sources

For each regulatory interaction, binding scores were calculated based on position matrix values or inserted from the original sources.

MatInspector within GEMS was used to scan transcription factor matrix matches in input sequences based on position weight matrices.

At the core of the processes is a method for TFBS prediction based on position weight matrices, known alternatively as position-specific scoring matrices (PSSMs, called 'possums'possums

This method is not expected to be as accurate as the prediction carried out here which is based on position weight matrices.

We show that better models can be obtained when we use information on the noninteracting peptides (negative examples), which is currently not used by the state-of-the art approaches based on position weight matrices.

Other technologies such as CHIP on chip array or in silico approaches based on position weight matrices can also be employed to identify putative transcription factor binding sites [ 92].

Further, we used z-scores of the total binding affinity (TBA), which uses a TF binding profile for the whole promoter based on position weight matrices (Molineris et al., 2011).

The majority of these tools were based on position weight matrices derived from results of in vitro approaches, namely competitive gel shift assays and SELEX, more recently integrated with results obtained from Chromatin immunoprecipitation experiments.

After applying RepeatMasker [ 57], we used the MATCH program of TRANSFAC [ 58] (version 9.2) to scan the sequences for the presence of transcription factor binding sites based on position weight matrices.

We build specialized models for each human SH3 domain and achieve competitive predictive performance of 0.73 area under precision-recall curve, compared with 0.27 area under precision-recall curve for state-of-the-art methods based on position weight matrices.

A search for NF-κB and STAT binding sites in the Nos2 gene body and 50 kB upstream sequence based on position weight matrices from the JASPAR database revealed consensus NF-κB sequences slightly downstream of the TSS and two peaks in the distal enhancer (marked with an asterisk in Figure 2E).