Sentence examples for motif analysis with from inspiring English sources

Homologous groups of genes (tBLASTx scores >170) from the other trypanosomatids analysed were also collected into clusters, their UTR sequences estimated using Splicemodel and masked using Tandem Repeat Finder [61], and finally used as input for motif analysis with Trawler.

Uncapped 5′-ends with a P-value less than 10-5 were selected for motif analysis with the MEME suite.

To further consolidate the differences between pre-MBT and MBT genes, we performed de novo motif analysis with MEME on the 200 bp centered on the transcription start site.

Motif analysis with InterProScan [ 25] revealed that the predicted proteins contained a MULE transposase domain as usually found in the Mutator superfamily of transposable elements [ 11, 12, 26], in addition to a FAR1 DNA binding domain and a SWIM-type Zinc finger motif (Additional file 5: Table S4).

In order to do so, we systematically performed a differential motif analysis with the program peak-motifs (RSAT) [ 27, 28] between the ChIP peaks located in non-coding regions associated (hereafter denoted "ZGA-peaks") and not associated ("non-ZGA peaks") with genes of the ZGA cluster (Additional file  10: Figure S7 and Additional file  11: Figure S8).

According to motif analysis with MEME-ChIP of top 100 genes based on FE, the most significant consensus sequences in ESC were characterized by a well-defined REST motif (RE1) composed of 5′AG[CG]ACCA[TC] GGACAG3′ (80 sites; E-value = 5.1 × 10−254) and a left half-site of RE1 composed of 5′[TG]TTCAGCAC[CT]3′ (21 sites; E-Value = 2.9 × 10−11) (Fig. 3A, B).

The putative complete sets of unique bZIPs from Chlamydomonas, Ostreococcus, Physcomitrella, black cottonwood, Arabidopsis and rice served as input for a conserved motif analysis performed with MEME (http://meme.sdsc.edu/meme/meme.html) [120].

CitMule Motif analysis performed with InterProScan.

Moreover, binding sites identified by such a sequence motif analysis come with a statistical confidence score and/or P-value.

Recent studies have shown that DHS motif analysis, along with digital footprints, can be used to generate potential regulatory networks directly [ 60].

Our phylogenetic reconstruction and motif analysis, together with the fact that PaNAC01 can functionally substitute for CUC2, indicate that PaNAC01 and CUC1 and CUC2 act in an evolutionarily conserved pathway.